I would really appreciate if someone could help out with this issue.
I have been battling the “Unexpected difference in fileset” issue since December 2018 when I unfortunately updated Duplicati 2.0.4.5_beta. Before the update it worked great for over a year. One of the early threads can be found here: Backups not running/error out after update to 2.0.4.5_beta_2018-11-28:
So far, my only course of action has been to recreate the backup(s) and start new. Repair, Recreate database have never worked. At this point, I have had to do this 6 times (I have 2 seperate computers running and 3 total backup routines). Just this week, 2 of my routines started doing giving me the error again and I am giving up until there is some type of update. For me, it takes about a month or so for the error to pop up on a new backup routine.