The source not listed in the scenes means bug in .json (during saving or whoever knows why, maybe "undo" bug...). For debugging purposes you may export your current Scene Collection and share it with the developers (if they wish too look at this bug themselves).
The next steps are optional.
After the export, restart OBS. Then try to click at the New file (empty field) of the Missing Files dialog window and click remove the file button (it appear only after you will click the empty field). Normally, there should appear new text saying <cleared>. Then you need to click Apply button to complete the changes. Just interesting how OBS will operate in your case.
As for the user, it will be much easier (?) to re-create the current set of the scenes (the scene collection) from the backup copy that you made manually long time ago (you did it, yeah? I'm sure...). And after the creation of the new scene collection complete, you may remove the troublesome.