Welcome to DEVONthink.
I have no experience with encryption keys not working as expected, but just working through what you say it is indeed a mystery, and a mystery why the “clean” not active. My hunch is that there is not yet a successful upload of the files (neither databases nor backups, by the way) DEVONthink needs to sync. So, if I were in this situation, I would:
- Do the “remove location” action on the Apple CloudKit location. “Clean” or whatever you see on the iPhone. This will allow you to start fresh.
- on Mac setup sync again to Apple CloudKit, Select one or more databases to sync. Should start the sync automatically (see the spinning ball). This puts something into Apple’s CloudKit servers. The time it takes depends on the size of your databases and any network throttling that Apple may chose to do.
- After complete, then setup sync on iPhone pointing to Apple CloudKit with same credentials, of course.
Also, please consider using Bonjour for synching. Will work quickly and more reliably than using any Third Party internet sync servers. As it’s Bonjour, works only when on the same local network. You can have both Bonjour and Apple CloudKit configured.
See @BLUEFROG’s explanation at Bonjour Simplified and of course refer to the outstanding DEVONthink Handbook.