That's a strange error, it means the read() systemcall is failing for some file in your calibre library. I have no idea what could cause that. General things to try are run the check library tool in calibre, run a chkdsk on the hard disk on which your calibre library is located, try moving your calibre library to another disk.
If none of those work, you can always just manually export your calibre library as described in the note here:
https://manual.calibre-ebook.com/faq...ter-to-another