Manually alter or delete backend files could corrupt or destroy your backup data. A compact operation can combine data from older backup files to a new DBLOCK file. This results in a file with a recent creation date, but it contains data from older backups.
A safer way is to do a full recreate of the database.
First, click on your backup name and click “Database” under “Advanced …”. Make a copy of the .sqlite file (specified in the “Location” section).
Then click the button “Recreate (delete and repair)”. This will initiate a full database recreation without affecting your backup files.
Recreating the database solved this issue for me.