I just updated to DT3 on my Mac, closed the iCloud Legacy sync database, and started a new iCloud CloudKit database, which is currently uploading.
I plan to set up DDTG3 on my iPad/iPhone and connect to the new CloudKit database. However, all of my documents have already synced from DDGT2.
So, my concern is that if I try to sync DDTG3 to the CloudKit database, I will end up with duplicates of all of my documents: one copy from DDTG2, and one copy from CloudKit.
I don’t think you need to do anything, other than relax.
DEVONthink will intelligently avoid duplicates, and identify that the same database is being synchronised, despite the carrier mechanisms.
The upload is (as I understand it) filling a new intermediary conduit. When something syncs from that new space, it will simply skip items it has already seen.
It’s how you can also have LAN syncing in operation as well, whilst avoiding duplicates.