### Please provide any additional information below.
The problem was on several disks, different manufacturer, different disk size, etc. The fsck always transformed hashA -> hashB, so the hashes were equal before and after the fsck run on all disks, though the link to the "old" file was not fixed to point to the "new" file.
### Have you had any luck using git-annex before? (Sometimes we get tired of reading bug reports all day and a lil' positive end note does wonders)
I use annex for years now, never had a problem with it. It is one of the most awesome pieces of software I've seen in the last 10 years, though I only use a really small part of it. Sometimes it bugs me a little that it consumes quite a lot of memory on large repositories, though most of the time this is not an issue for me.