Were those two files with the reduced sizes always on the FTP destination, put there by Duplicati directly?
What OS is the destination? Does the FTP server keep any logs that would show FTP history for the files?
You mentioned a filesystem error. I wonder if these two files could have suffered damage, however usually when files shrink, I find their sizes go down to a nice even binary size (like filesystem may do). Yours didn’t.
What yours did do is shrink by about 1 in 200 or 300 characters, so I almost wonder if FTP worked in ASCII mode instead of binary mode for some reason. FTP has reliability drawbacks and ways to make short files, however if I read Duplicati code correctly, I think this says the files were originally right-sized, but not now…
You could look at the dates on those files, and if you still have a good local database, the dates are inside it along with other information like the expected file size and hash value that you’re getting complaints about.
You can sanity-test the files yourself by trying to decrypt with SharpAESCrypt.exe or AES Crypt. Directions. Damaged dindex files can be replaced if database is sound, but damaged dblocks are lost source file data.
Could you share some information about your main goal? Are you trying to restore due to lost source data? Especially when the remote backup files are damaged (with likely data loss), doing repairs can face issues.