Just for the record: your cc.db is indeed the culprit. Well, actually, the books seem to be. All of your books have NULL "CDE Key" (=ASIN or UUID) and "CDE Type" (=usually "EBOK", "PDOC" etc.) values. Since these are the values which are used inside the collections.json file, it is normal that the books can't be found.
However, it's beyond me WHY these values are null. That's definitely not normal. Are you using some funky plugin or other settings, which might remove this required
metadata from your books?
PS: The cc.db is a simple SQLite database, so you can take a look at it for yourself, using any tool that can handle SQLite DBs.
PPS: You can check the book metadata using gluggy's Mobi Metadata Editor