Using Apple’s CloudKit. I suspected that. You’ll find from posts on this forum that Apple’s sync services are unreliable for many people. Looks like you are one of those who sadly experience poor service from Apple. This type of sync unreliability, based on information other internet forums, is not limited to the DEVONthink world, but troubles other apps.
If you really need syncing via third party internet services, Dropbox is reliable. There are technical reasons why Dropbox more reliable than Apple’s which you can read about in the posts if you need to.
I rely on Bonjour to sync two Macs and two iOS devices. Bonjour does not involve using the Internet and a local WebDav service on my Synology NAS. Bonjour quick and very reliable. I also have Dropbox syncing one database–my “works in progress” database. All this just works and does not need hours of fiddling and researching.