@Mortlach: That's not an error, that's a warning, and it's already pretty self-explanatory:
The collections have been edited on the Kindle since the last time you used the plugin, but some of those edits are pointing to a book that's no longer on your Kindle. (Or that the plugin didn't find).
Those 'missing' books wouldn't happen to be KF8 files? That would explain it, if you're using the latest official release, and not my patched version