@raiannon: First of all, be aware that you *will* have to JB the PW in order to do anything with Collections
.
Second, if some collections are unchanged, you won't get anything about it in the review report, so I'm guessing that it's as simple as that, and everything's fine
.
(If what's on Calibre's side is important anyway, you could also simply clear the collections on the Kindle and reexport them).