diff --git a/cura/CuraApplication.py b/cura/CuraApplication.py
index 2f0b1594cd..58bc7704e9 100755
--- a/cura/CuraApplication.py
+++ b/cura/CuraApplication.py
@@ -458,15 +458,16 @@ class CuraApplication(QtApplication):
 
         self._version_upgrade_manager.setCurrentVersions(
             {
-                ("quality", InstanceContainer.Version * 1000000 + self.SettingVersion):             (self.ResourceTypes.QualityInstanceContainer, "application/x-uranium-instancecontainer"),
-                ("quality_changes", InstanceContainer.Version * 1000000 + self.SettingVersion):     (self.ResourceTypes.QualityChangesInstanceContainer, "application/x-uranium-instancecontainer"),
-                ("intent", InstanceContainer.Version * 1000000 + self.SettingVersion):              (self.ResourceTypes.IntentInstanceContainer, "application/x-uranium-instancecontainer"),
-                ("machine_stack", GlobalStack.Version * 1000000 + self.SettingVersion):             (self.ResourceTypes.MachineStack, "application/x-cura-globalstack"),
-                ("extruder_train", ExtruderStack.Version * 1000000 + self.SettingVersion):          (self.ResourceTypes.ExtruderStack, "application/x-cura-extruderstack"),
-                ("preferences", Preferences.Version * 1000000 + self.SettingVersion):               (Resources.Preferences, "application/x-uranium-preferences"),
-                ("user", InstanceContainer.Version * 1000000 + self.SettingVersion):                (self.ResourceTypes.UserInstanceContainer, "application/x-uranium-instancecontainer"),
-                ("definition_changes", InstanceContainer.Version * 1000000 + self.SettingVersion):  (self.ResourceTypes.DefinitionChangesContainer, "application/x-uranium-instancecontainer"),
-                ("variant", InstanceContainer.Version * 1000000 + self.SettingVersion):             (self.ResourceTypes.VariantInstanceContainer, "application/x-uranium-instancecontainer"),
+                ("quality", InstanceContainer.Version * 1000000 + self.SettingVersion):                         (self.ResourceTypes.QualityInstanceContainer, "application/x-uranium-instancecontainer"),
+                ("quality_changes", InstanceContainer.Version * 1000000 + self.SettingVersion):                 (self.ResourceTypes.QualityChangesInstanceContainer, "application/x-uranium-instancecontainer"),
+                ("intent", InstanceContainer.Version * 1000000 + self.SettingVersion):                          (self.ResourceTypes.IntentInstanceContainer, "application/x-uranium-instancecontainer"),
+                ("machine_stack", GlobalStack.Version * 1000000 + self.SettingVersion):                         (self.ResourceTypes.MachineStack, "application/x-cura-globalstack"),
+                ("extruder_train", ExtruderStack.Version * 1000000 + self.SettingVersion):                      (self.ResourceTypes.ExtruderStack, "application/x-cura-extruderstack"),
+                ("preferences", Preferences.Version * 1000000 + self.SettingVersion):                           (Resources.Preferences, "application/x-uranium-preferences"),
+                ("user", InstanceContainer.Version * 1000000 + self.SettingVersion):                            (self.ResourceTypes.UserInstanceContainer, "application/x-uranium-instancecontainer"),
+                ("definition_changes", InstanceContainer.Version * 1000000 + self.SettingVersion):              (self.ResourceTypes.DefinitionChangesContainer, "application/x-uranium-instancecontainer"),
+                ("variant", InstanceContainer.Version * 1000000 + self.SettingVersion):                         (self.ResourceTypes.VariantInstanceContainer, "application/x-uranium-instancecontainer"),
+                ("setting_visibility", SettingVisibilityPresetsModel.Version * 1000000 + self.SettingVersion):  (self.ResourceTypes.SettingVisibilityPreset, "application/x-uranium-preferences"),
             }
         )
 
diff --git a/cura/Machines/Models/SettingVisibilityPresetsModel.py b/cura/Machines/Models/SettingVisibilityPresetsModel.py
index 6b5766c127..d268774850 100644
--- a/cura/Machines/Models/SettingVisibilityPresetsModel.py
+++ b/cura/Machines/Models/SettingVisibilityPresetsModel.py
@@ -19,6 +19,8 @@ class SettingVisibilityPresetsModel(QObject):
     onItemsChanged = pyqtSignal()
     activePresetChanged = pyqtSignal()
 
+    Version = 2
+
     def __init__(self, preferences: Preferences, parent = None) -> None:
         super().__init__(parent)
 
diff --git a/plugins/PostProcessingPlugin/scripts/DisplayProgressOnLCD.py b/plugins/PostProcessingPlugin/scripts/DisplayProgressOnLCD.py
index e39e69eff0..fd1c8af004 100644
--- a/plugins/PostProcessingPlugin/scripts/DisplayProgressOnLCD.py
+++ b/plugins/PostProcessingPlugin/scripts/DisplayProgressOnLCD.py
@@ -77,7 +77,7 @@ class DisplayProgressOnLCD(Script):
             current_time_string = "{:d}h{:02d}m{:02d}s".format(int(h), int(m), int(s))
             # And now insert that into the GCODE
             lines.insert(line_index, "M117 Time Left {}".format(current_time_string))
-        else:  # Must be m73.
+        else:
             mins = int(60 * h + m + s / 30)
             lines.insert(line_index, "M73 R{}".format(mins))
 
diff --git a/plugins/VersionUpgrade/VersionUpgrade48to49/VersionUpgrade48to49.py b/plugins/VersionUpgrade/VersionUpgrade48to49/VersionUpgrade48to49.py
new file mode 100644
index 0000000000..789830ef08
--- /dev/null
+++ b/plugins/VersionUpgrade/VersionUpgrade48to49/VersionUpgrade48to49.py
@@ -0,0 +1,110 @@
+# Copyright (c) 2021 Ultimaker B.V.
+# Cura is released under the terms of the LGPLv3 or higher.
+
+import configparser
+from typing import Tuple, List
+import io
+
+from UM.VersionUpgrade import VersionUpgrade
+
+
+class VersionUpgrade48to49(VersionUpgrade):
+    _moved_visibility_settings = ["top_bottom_extruder_nr", "top_bottom_thickness", "top_thickness", "top_layers",
+                                  "bottom_thickness", "bottom_layers", "ironing_enabled"]
+
+    def upgradePreferences(self, serialized: str, filename: str) -> Tuple[List[str], List[str]]:
+        """
+        Upgrades preferences to have the new version number.
+        :param serialized: The original contents of the preferences file.
+        :param filename: The file name of the preferences file.
+        :return: A list of new file names, and a list of the new contents for
+        those files.
+        """
+        parser = configparser.ConfigParser(interpolation = None)
+        parser.read_string(serialized)
+
+        # Update version number.
+        parser["general"]["version"] = "7"
+
+        # Update visibility settings to include new top_bottom category
+        parser["general"]["visible_settings"] += ";top_bottom"
+
+        if any([setting in parser["cura"]["categories_expanded"] for setting in self._moved_visibility_settings]):
+            parser["cura"]["categories_expanded"] += ";top_bottom"
+
+        result = io.StringIO()
+        parser.write(result)
+        return [filename], [result.getvalue()]
+
+    def upgradeStack(self, serialized: str, filename: str) -> Tuple[List[str], List[str]]:
+        """
+        Upgrades stacks to have the new version number.
+
+        This updates the post-processing scripts with new parameters.
+        :param serialized: The original contents of the stack.
+        :param filename: The original file name of the stack.
+        :return: A list of new file names, and a list of the new contents for
+        those files.
+        """
+        parser = configparser.ConfigParser(interpolation = None)
+        parser.read_string(serialized)
+
+        # Update version number.
+        if "general" not in parser:
+            parser["general"] = {}
+        parser["general"]["version"] = "5"
+
+        # Update Display Progress on LCD script parameters if present.
+        if "post_processing_scripts" in parser["metadata"]:
+            new_scripts_entries = []
+            for script_str in parser["metadata"]["post_processing_scripts"].split("\n"):
+                if not script_str:
+                    continue
+                script_str = script_str.replace(r"\\\n", "\n").replace(r"\\\\", "\\\\")  # Unescape escape sequences.
+                script_parser = configparser.ConfigParser(interpolation=None)
+                script_parser.optionxform = str  # type: ignore  # Don't transform the setting keys as they are case-sensitive.
+                script_parser.read_string(script_str)
+
+                # Update Display Progress on LCD parameters.
+                script_id = script_parser.sections()[0]
+                if script_id == "DisplayProgressOnLCD":
+                    script_parser[script_id]["time_remaining_method"] = "m117" if script_parser[script_id]["time_remaining"] == "True" else "none"
+
+                script_io = io.StringIO()
+                script_parser.write(script_io)
+                script_str = script_io.getvalue()
+                script_str = script_str.replace("\\\\", r"\\\\").replace("\n", r"\\\n")  # Escape newlines because configparser sees those as section delimiters.
+                new_scripts_entries.append(script_str)
+            parser["metadata"]["post_processing_scripts"] = "\n".join(new_scripts_entries)
+
+        result = io.StringIO()
+        parser.write(result)
+        return [filename], [result.getvalue()]
+
+    def upgradeSettingVisibility(self, serialized: str, filename: str) -> Tuple[List[str], List[str]]:
+        """
+        Upgrades setting visibility to have a version number and move moved settings to a different category
+
+        :param serialized: The original contents of the stack.
+        :param filename: The original file name of the stack.
+        :return: A list of new file names, and a list of the new contents for
+        those files.
+        """
+        parser = configparser.ConfigParser(interpolation = None, allow_no_value=True)
+        parser.read_string(serialized)
+
+        # add version number for the first time
+        parser["general"]["version"] = "2"
+
+        if "top_bottom" not in parser:
+            parser["top_bottom"] = {}
+
+        if "shell" in parser:
+            for setting in parser["shell"]:
+                if setting in self._moved_visibility_settings:
+                    parser["top_bottom"][setting] = None
+                    del parser["shell"][setting]
+
+        result = io.StringIO()
+        parser.write(result)
+        return [filename], [result.getvalue()]
diff --git a/plugins/VersionUpgrade/VersionUpgrade48to49/__init__.py b/plugins/VersionUpgrade/VersionUpgrade48to49/__init__.py
new file mode 100644
index 0000000000..fd46dd8123
--- /dev/null
+++ b/plugins/VersionUpgrade/VersionUpgrade48to49/__init__.py
@@ -0,0 +1,44 @@
+# Copyright (c) 2020 Ultimaker B.V.
+# Cura is released under the terms of the LGPLv3 or higher.
+
+from typing import Any, Dict, TYPE_CHECKING
+
+from . import VersionUpgrade48to49
+
+if TYPE_CHECKING:
+    from UM.Application import Application
+
+upgrade = VersionUpgrade48to49.VersionUpgrade48to49()
+
+def getMetaData() -> Dict[str, Any]:
+    return {
+        "version_upgrade": {
+            # From                           To                              Upgrade function
+            ("preferences", 6000016):        ("preferences", 7000016,        upgrade.upgradePreferences),
+            ("machine_stack", 4000016):      ("machine_stack", 5000016,      upgrade.upgradeStack),
+            ("extruder_train", 4000016):     ("extruder_train", 5000016,     upgrade.upgradeStack),
+            ("setting_visibility", 1000000): ("setting_visibility", 2000016, upgrade.upgradeSettingVisibility),
+        },
+        "sources": {
+            "preferences": {
+                "get_version": upgrade.getCfgVersion,
+                "location": {"."}
+            },
+            "machine_stack": {
+                "get_version": upgrade.getCfgVersion,
+                "location": {"./machine_instances"}
+            },
+            "extruder_train": {
+                "get_version": upgrade.getCfgVersion,
+                "location": {"./extruders"}
+            },
+            "setting_visibility": {
+                "get_version": upgrade.getCfgVersion,
+                "location": {"./setting_visibility"}
+            }
+        }
+    }
+
+
+def register(app: "Application") -> Dict[str, Any]:
+    return {"version_upgrade": upgrade}
diff --git a/plugins/VersionUpgrade/VersionUpgrade48to49/plugin.json b/plugins/VersionUpgrade/VersionUpgrade48to49/plugin.json
new file mode 100644
index 0000000000..1e12cbf4b0
--- /dev/null
+++ b/plugins/VersionUpgrade/VersionUpgrade48to49/plugin.json
@@ -0,0 +1,8 @@
+{
+    "name": "Version Upgrade 4.8 to 4.9",
+    "author": "Ultimaker B.V.",
+    "version": "1.0.0",
+    "description": "Upgrades configurations from Cura 4.8 to Cura 4.9.",
+    "api": "7.4.0",
+    "i18n-catalog": "cura"
+}
diff --git a/resources/bundled_packages/cura.json b/resources/bundled_packages/cura.json
index 6e191a1665..82587645e0 100644
--- a/resources/bundled_packages/cura.json
+++ b/resources/bundled_packages/cura.json
@@ -917,6 +917,40 @@
             }
         }
     },
+    "VersionUpgrade47to48": {
+        "package_info": {
+            "package_id": "VersionUpgrade47to48",
+            "package_type": "plugin",
+            "display_name": "Version Upgrade 4.7.0 to 4.8.0",
+            "description": "Upgrades configurations from Cura 4.7.0 to Cura 4.8.0",
+            "package_version": "1.0.0",
+            "sdk_version": "7.4.0",
+            "website": "https://ultimaker.com",
+            "author": {
+                "author_id": "UltimakerPackages",
+                "display_name": "Ultimaker B.V.",
+                "email": "plugins@ultimaker.com",
+                "website": "https://ultimaker.com"
+            }
+        }
+    },
+    "VersionUpgrade48to49": {
+        "package_info": {
+            "package_id": "VersionUpgrade48to49",
+            "package_type": "plugin",
+            "display_name": "Version Upgrade 4.8.0 to 4.9.0",
+            "description": "Upgrades configurations from Cura 4.8.0 to Cura 4.9.0",
+            "package_version": "1.0.0",
+            "sdk_version": "7.4.0",
+            "website": "https://ultimaker.com",
+            "author": {
+                "author_id": "UltimakerPackages",
+                "display_name": "Ultimaker B.V.",
+                "email": "plugins@ultimaker.com",
+                "website": "https://ultimaker.com"
+            }
+        }
+    },
     "X3DReader": {
         "package_info": {
             "package_id": "X3DReader",
@@ -1789,4 +1823,4 @@
             }
         }
     }
-}
\ No newline at end of file
+}
diff --git a/resources/setting_visibility/advanced.cfg b/resources/setting_visibility/advanced.cfg
index dd44df06e9..9198f390fc 100644
--- a/resources/setting_visibility/advanced.cfg
+++ b/resources/setting_visibility/advanced.cfg
@@ -1,6 +1,7 @@
 [general]
 name = Advanced
 weight = 2
+version = 2
 
 [machine_settings]
 
diff --git a/resources/setting_visibility/basic.cfg b/resources/setting_visibility/basic.cfg
index f23d498c7e..6952baee2a 100644
--- a/resources/setting_visibility/basic.cfg
+++ b/resources/setting_visibility/basic.cfg
@@ -1,6 +1,7 @@
 [general]
 name = Basic
 weight = 1
+version = 2
 
 [machine_settings]
 
diff --git a/resources/setting_visibility/expert.cfg b/resources/setting_visibility/expert.cfg
index 1ad90e5467..274433b7b2 100644
--- a/resources/setting_visibility/expert.cfg
+++ b/resources/setting_visibility/expert.cfg
@@ -1,6 +1,7 @@
 [general]
 name = Expert
 weight = 3
+version = 2
 
 [machine_settings]