avidgrapher
That is strange.
According to the description and also in my experience, files with this function are not write-protected.
Storage Scopes only makes the app guess that it can write anywhere and read anything, but it is only allowed to read and write in its scope and can/may only delete or write what it has written itself.
That's why you don't usually have to specify any special folders and/or files for Storage Scope.
Simply activate the function and you're done.
For Metro, however, I had to add the music folder so that the app could find my music files.
This could also be the case with Vanilla if the usual storage locations are not stored in the programme code or if you have selected a storage location that differs from the standard.
I can only imagine that this app now or generally wants to use more than one storage location (folder) and that this is outside the actually intended location (perhaps only happened after an update of the app?).
I'm not using Vanilla, but have good experience with Metro, a fork of Retro Music Player.
I used it to maintain my music collection and add covers from the Internet.
Changes (including deletions) were no problem despite Storage Scope.
It should actually be the same with Vanilla.