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The error message “File truncated – file may have been damaged” is most often seen server-side, but every once in a while it will turn up on client computers, especially where Notes is installed on a network share (not a good idea) and synchronised to the local machine through offline folders.
I have to say, this is one of the clearer error messages Notes has to offer. It basically means that there is a corrupt file. The file I’ve seen it happen to the most is desktop6.ndk. What this means is that unless there’s another copy of it, you lose all the links in your dashboard.
In my opinion, the simplest way to resolve the problem is replace the faulty file, either by copying in a (non-corrupted) copy of it, or by deleting it altogether, and letting Notes replace the file automatically.