Comment 3 for bug 739045

I'm using Calibre with git-annex

You should not be using WORM backend for books, it's for really large files, i.e. videos, books are not that large.
Use SHA1E backend, it's fast and checksums content and you do want to do it.

Calibre usually doesn't modify the stored books unless it's asked to update the books metadata by "Embed Metadata".

Perhaps you have enabled something in the preferences?
Look into the Kobo device backend config, maybe there is something like metadata sync.