Regression: Several project settings, especially from built-in Plugins, are being silently erased when previously they were not, which is perceived as a bug

In UE's Project Settings, some pages are saved automatically to the project's "Config/Default<CATEGORY>.ini" file (meant to be version-controlled) on every change. Other pages have buttons "Set as Default" and "Reset to Defaults" on the header, and they are only saved/loaded to the default config files by clicking these buttons.

Up to UE 5.3, when the user made changes to property pages of the second type, UE would automatically save every change to the "Saved/Config/<CATEGORY>.ini" file (not meant to be version-controlled), so that those changes would be persisted from one editor session to the next, while allowing the user to make the changes "official" or reset them through the buttons mentioned before. However, starting with UE 5.4, these settings are no longer automatically saved to the "Saved/Config" folder unless their sections are explicitly opted-in by being added to a special [SectionsToSave] section somewhere up in the config file hierarchy. This behavior was activated by CL 29098706 in ue5-main branch (which mentions that this system "massively reduces what settings are saved in Saved/Config").

The problem is that several project settings, especially from built-in plugins, were not changed to be treated as the first kind, and neither had their sections added to [SectionsToSave]. Because of that, changes made by the user are not saved at all now unless they set them as default through the button on the header. When they close and reopen the editor, it seems to them that the settings were simply silently erased. This has been reported as a bug by at least 3 licensees, 2 of them in february 2025. While it is possible for them to click "Set as Default" and/or to manually add the desired sections to [SectionsToSave], it does not seem right to "erase" any settings they manually configured. Moreover, this was never needed before and there is nothing in the Project Settings pages bringing attention to it.

Note that, since the CL mentioned above, some settings have been added to [SectionsToSave] (see CL 30216578 in ue-5 branch and CL 32766089 in 5.4 branch), but many others haven't.

Some examples of affected settings reported by licensees as having been erased:

[/Script/Engine.PlayerInput]
[/Script/ConcertClient.ConcertClientConfig]
[/Script/UdpMessaging.UdpMessagingSettings]

1. Open any project in the editor
2. Enable the Multi-User Editing plugin
3. Go to the Project Settings and make some changes to these pages:
3.1. Multi-User Editing
3.2. TCP Messaging
3.3. UDP Messaging
4. Restart the Editor and check that the settings were all lost