First step might be to go through “Sync Issues” section in DEVONthink Handbook (page 177 in version 3.6.3) and see if doing things suggested there helps.
I could be wrong, but I doubt a re-build will help syncing, unless the database(s) is(are) corrupted. First see page 181 of the DEVONthink Handbook on repairing a defective database. Then perhaps “Verify and Repair” taking care and report to note any messages in Log. Then perhaps “clean” the CloudKit location of the sync files followed by turning synch back on and let the sync complete. Take note and report any messages in Log. If any messages in Log, search this forum for those words and see if there is any ideas there.
Me, I’d get synching going by Bonjour method first as it’s simpler to setup, faster, and more reliable than using Apple’s CloudKit. Once working, you can rely on it (via Local Network) and get Apple’s CloudKit going as you find time. Bonjour setup covered in the DEVONthink Handbook, along with supplementary info at Bonjour Simplified
Finally, work on only one database at a time, initially to keep the bytes needed to be moved low. And don’t sync stuff that you really don’t need to be synched.