Box sets can be tricky because MusicBrainz is more likley to have the original albums comprising the box set then the box set itself, ialso ts not always clear from the way user files are organized if they have the box set or the original albums.
First thing note that in SongKong you can just select a subfolder and Undo Changes for that, so that may be an idea in this case. Secondly can you give me the details of the box set so I can check your report and see what has happened.
You could just modify the metadata with SongKongs Manual Edit, I think you would just need to modify Album so same for all songs on the box set, set Disc No so correct for each disc and set Disc Total to the same for all songs, then rescan the folders with Roon.