Looks a lot like the other-topic situation where the fileset referenced non-existent files. Repeating here:
SELECT * FROM "FilesetEntry" LEFT JOIN "FixedFile" ON "FilesetEntry"."FileID" = "FixedFile"."ID" WHERE "FilesetEntry"."FilesetID" = 5 AND "FixedFile"."ID" IS NULL
If using an original database, refer to File view instead of FixedFile table in the database bug report.
Result table has 65 rows, probably corresponding to 65 reduction of calculated files versus fileset’s list:
is 65 short from the complex query that looks for data bits compared to the simple expected fileset list.
Above query (if I’m doing this right) means that again some records of old files got removed somehow.
looks like it might be trying to look in the other direction (if fileset had extras). EXISTS is also suspect, although all this comment is tentative. Regardless the query did not return any rows when I had run it.