“Unexpected difference in fileset” test case and code clue #3800 led to fix below in the following release: v2.0.4.22-2.0.4.22_canary_2019-06-30
Fixed data corruption caused by compacting, thanks @ts678 and @warwickmm
which unfortunately was after v2.0.4.21-2.0.4.21_experimental_2019-06-28, which didn’t become a beta.
You can check your job log from the backup before your problem to see if compact shows any statistics.
If so, one avoidance of a repetition is to set –no-auto-compact=true (which prevents re-use of free space) or install a fixed version. 2.0.4.22 did well over two months of testing, however 2.0.4.28 canary is the latest canary. If it does well (probably over a shorter period of testing), then it will likely lead to beta at some point.
Note that due to database format updates, downgrading (e.g. to 2.0.4.23 which is basically 2.0.4.5) is hard, but upgrade to next feature beta (or experimental) should work. You should also change your Settings to a more stable channel (Beta for example) if you install Canary. You can change to Canary temporarily if you want to upgrade that way (instead of using full installer), then change it back before a broken canary ships.
EDIT: Upgrading would be to avoid future problems. Current problem is dealt with (or not) as shown earlier.