Just try it on one and check whether this fixes the issue of the preferences.
10-4. Will report back
MacBook-Air-2:~ samuelcooper$ defaults delete com.devon-technologies.think3
2019-07-25 05:48:12.275 defaults[7525:1771804]
Domain (com.devon-technologies.think3) not found.
Defaults have not been changed.
Is that a normal response?
No, definitely not. If you’ve already used DEVONthink 3 on this account then there should be definitely such preferences and the command should be successful. Where is DEVONthink 3 installed?
I’d suggest to download the app again and to replace the installed version.
I’m still having issues getting it to stay synced between my two computers. This is after reinstalling it on both computers. Not sure what else to do. Currently exporting all of my databases and thinking of deleting everything and starting over unless you have a better idea.
Just curious: under iCloud setting, there is an option to use iCloud for ur Desktop and Documents Folders. If you have checked this option and/or have checked “Optimise Mac Storage”, it means you are virtually syncing/storing all of your older/unused documents with iCloud. AND if ur databases are also located in those Desktop and Documents Folders, there might be a problem? As far as I am aware, DT has repeatedly warned users not to put their database on any cloud drive? (better to wait for DT to confirm my curiosity that might be one possible source of your issues…)
A screen capture showing some of the problematic indexed files in the Finder may prove helpful.
My databases are located at the same level as documents or desktop, so they shouldn’t be getting indexed. I don’t think you’re even able to set up your databases in either of those locations for that reason. I meant the documents or folders that my database is indexing.
The other screenshots already show it. I’ll have a database with that name that is empty aside from the three groups that are in every database, no files in there, and then listed as remote I’ll have database by the same name (which should be syncing via icloud) sometimes multiple ones. One of these that has my files in it but they aren’t communicating the way that they should be.
For the life of me I can’t get these databases to sync. I don’t know if I’m doing something wrong or what.
Files either get sent all outside of their file structure and orphaned, or they just aren’t in the database at all.
I’ll be able to access them from the other computer, but despite verifying that sync is turned on and then closing everything out on that computer it won’t sync with my laptop. I’ve tried it with devonthink closed on one computer, open, it doesn’t matter, I still can’t get it to sync, if anything it just shows with more remote versions, that wont upload onto my laptop.
I’m no longer getting the settings that are randomly resetting themselves, but I’m not getting databases to sync either.
This is from my laptop
This is what is listed under remote on my laptop from the sync setting
Notice the duplicates. If I were to click on any of these and do either the quick or the thorough verification they will verify
This is from my iMac
Notice no duplicates. The databases that are listed here that aren’t listed under my macbooks listing either aren’t used or aren’t synced for various reasons and are therefore intended to stay on the iMac.
I don’t want to play around too much with cleaning or overiding one database for another until I know what’s going on because I don’t want to accidentally delete anything.
This is view from that same database that’s on my iMac
The other screenshots already show it.
I see no screencap showing the indexed files in the Finder.
Hold the Option key and choose Help > Report bug to start a support ticket.
I think it may have resolved itself, fingers crossed. By resolved itself I mean I had to spend a good long while on the phone with Apple trying to figure out what was going on with my computer overall. I was noticing odd behavior in other apps as well, just generally speaking, not just in Devonthink.
All of my permissions and everything else has been reset, so I’m going to play around with everything and see if that did the trick, and if not I will definitely open up a help ticket to hopefully take care of it that way then.
I just wanted to make sure that I said thanks again for always just being super responsive and patient in general. I’m sure I probably wasn’t doing the best job in communicating what my actual underlying issue was and when I do figure it out there will be some crazy simple explanation and solution.
Seriously though, as someone not necessarily the most graceful or intuitive when it comes to computers, you and this community definitely make me feel like lifelines are out there and available, which is the only way I feel comfortable enough to try different things.
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Fingers crossed for you and thanks for the nice comments! 
I was just thinking the same thing - amazing level of support!
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