TL;Dr; Lots of random thoughts during the process… Result: Inconclusive.
If a dindex file goes missing, Repair is supposed to rebuild it from database. Are yours missing content?
Well, I just said that I’ve seen those 541 bytes files so many times. I’ve never checked what’s inside but my guess was totally correct. 541 bytes i-file - Decrypted 232 bytes (zipped) - Unzipped 146 bytes manifest. Content:
{"Version":2,"Created":"20180627T164703Z","Encoding":"utf8","Blocksize":102400,"BlockHash":"SHA256","FileHash":"SHA256","AppVersion":"2.0.2.1"}
Usually after that I’ve got bad expectations about restorability. Even if test (100%) says all is good, when running full restore test it’s likely to fail. (No i didn’t check this time, this is gut feeling and I usually do it like this). Usually best approach is to delete the database and rebuild it and only then next backup will fill in probably lost blocks.
This might be initially caused by the broken compact. Just my best guess so far.
Yet I just realized this was a bad approach. Because this file might not be created by repair, this might be empty file uploaded by Duplicati, because I’ve configured it to upload empty files… I’ll need to dig up the repair 541 byte file, next time I’ll encounter one.