I had this one pretty regularly, also working parallely on two systems.
You don't have to touch every single citation. You have to go into the
bibliography-entry in your lyx file (i. e., the field linking to the
bibtex-file, the one you insert at the place where you want the
bibliography to
Uups, the last one went off too early.
I also had these kind of errors and often found them caused by bibtex-related
problems, mostly special characters.
Instead of actually splitting your document in search for the error I turn
document parts into comments, which is easily undoable.
Kind regards