Originally Posted by EightWeight
The corrupt files were in .Trash-1000, so I deleted that whole thing and now Calibre connects to it.
IIRC the .Trash-1000 dir is created by a linux file manager (don't remember which one) for "recycle bin" purposes. 1000 is probably the UID.
This "feature" can also end up taking non-trivial amounts of space on flash media (kindles, USB sticks, etc).
When it was filling my wife's mp3 player up I deleted the dir and set her file manager to not use trashcan/recycle functionality.