Apply changed visible settings to preferences file

Otherwise the change will not be made to the actual file, just in memory.

Contributes to issue CURA-6311.

plugins/VersionUpgrade/VersionUpgrade41to42/VersionUpgrade41to42.py

@@ -72,6 +72,7 @@ class VersionUpgrade41to42(VersionUpgrade):
                 if old_name in visible_settings:
                     visible_settings.remove(old_name)
                     visible_settings.add(new_name)
+            parser["general"]["visible_settings"] = ";".join(visible_settings)
 
         result = io.StringIO()
         parser.write(result)