I think I’m one of the few people in these forums who doesn’t gripe about CloudKit at every opportunity . I’m successfully using it for multiple devices (discussed in a different forum posting). To give you an idea of how much data I’m sync’ing, if I look at the Settings panel on my iPhone and look into iCloud Storage usage by different apps, DEVONthink is using a total of 90 GB. So, from the perspective of someone who uses it successfully, here are a few ideas about the problems you’re experiencing:
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One thing that may make a big difference is the speed and nature of your internet connection. Is it possible that your connection to the wider internet (specifically to reach Apple’s servers) is relatively slow, or saturated from traffic from other devices, or unreliable? You would probably know this from your personal experiences in general, and from clues such as whether the performance of other network-heavy applications seems slow (e.g., whether you can play videos smoothly or whether there are a lot of pauses). You could also test your network speed using various sites on the net that offer free speed tests (e.g., https://www.speedtest.net – this is not an endorsement of that site, just an example).
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Have you tried the step of cleaning the DEVONthink sync destination, deleting the database(s) from your iOS device, and letting your iOS device re-download the database from a clean starting point? (Note this is different from recreating the database.)
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Not knowing anything about the state of your devices, is it possible your mac and/or iOS device are old and slow (kind of like me)? The mac is probably fine unless you have a very old machine, but I remember when I was using my iPhone 6S a couple of years ago before finally getting a new one, it struggled – and in fact, I couldn’t sync all my databases because the phone didn’t have enough storage space. I think DEVONthink will run on probably all macs and phones and ipads; however, performance problems may contribute to the symptoms you’re seeing.
Some of the things mentioned above may be outside your control, but IMHO it’s still important to consider some of these variables when trying to identify the root cause of a problem.