Writing on behalf of a friend, so might have to get back w/ followups, but this is what happened:
After DT update on 2 bonjour synced macs, the databases under the sync tab would not appear anymore, so she turned on/off bonjour incoming connections on both computers to see if that would fix it. When she was working in Obsidian, links weren’t working and she realized that the files no longer existed. But the files were not in trash. Duplicate w/ conflicts is set in sync settings. (Possibly separate issue, there were other folders in trash that she says she didn’t delete)
Looking in backed up databases (one from this morning before all this started happening), the files were also gone, but not sure if that could be a syncing issue because she changed the database name before opening. Don’t know the order of events, but she suddenly had duplicate research databases, and then the entire database disappeared on one computer.
Then she started getting duplicate database UUID in the log and at one point, these messages were just running endlessly. When she unplugged the backup drive, this error went away.
We did a verify database, but on one computer there was a missing file. We deleted that file, but she’s afraid to empty the trash because it’s quite full and she doesn’t want to permanently lose work.
Bottom line, she’s having a bit of a freakout cause all of a sudden, months of work seems to be gone and not sure how to help. Any ideas or follouwp questions I can ask.
Thanks for the help!!!
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This does not sound like the products of syncing. Databases going missing and duplicate database UUIDs, typically caused by copying databases in the Finder and opening them at the same time, are part of no sync process.
Does she have some other syncing application running, e.g., to an NAS?
Thanks for the quick reply… but the UUIDs happened after the first set of issues when she tried to look at backups to see if the files were there… but the first part all happened before when she turned on/off bonjour to see if that would get her databases to show up in the sync list.
You’re welcome.
Gotcha on the duplicate UUID. That makes more sense.
Dis/enabling Bonjour wouldn’t cause databases to go missing.
Did she have databases on one mac she was trying to import to the other?
hello… so, originally she was syncing the same database across two computers w/ bonjour… she says she saw files dissapear in front of her eyes, so I was suspecting maybe there was some syncing issue, but not sure what it could be. In what cases can that happen and is there any way to find her missing files if they are not in the trash? some of them are missing from months ago and some recently.
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Hello and thanks again. I have more info that hopefully will help. First off, yes, some things are indexed most/all on iCloud. That said, she’s finding that when clicking on a group/folder in DT and tries to reveal it in the finder, some of the folder exist on her hard drive (but not in the database, just on her hard drive somewhere), but the containing folders that she can see in DT do not exist in the revealed local folder. However, when she reveals the location of one of the containing folders in DT, those folders do exist in iCloud.
So, she has some files & folders in the database, some on her hard drive outside the database, and also in iCloud. But the problem with files is only the ones on iCloud. And often, when she clicks on a file in DT that does exist on iCloud, it instantly disappears in front of her eyes in DT. This also applies to replicants.
There are so many files she can’t manually figure out which ones are missing, so the question is how can she recover/reconnect all the files (that thankfully are actually there in iCloud) as well as the replicants that have also disappearing when she clicks on them? But also, she doesn’t want to use indexing anymore after this. Should she rebuild the database, or drag the files to the desktop, or is there a way to bring in the indexed files into the database? She’s hoping she doesn’t lose months of work if she can’t get back her files and replicants and other connections she’s made between files and folders.
She’s pretty desperate to fix this as there are many files missing and she can’t be sure which ones will turn up missing when she does searches for terms in her books and pdfs, which is how she’s discovering that certain files are missing. That is, either the term doesn’t include the missing docs, or they do, but when she clicks on them they disappear.
Thanks in advance!
R
p.s. this all started happening after the update and the bonjour not working properly, but not sure if this is just an indexing issue w/ icloud or also to do with the update and bonjour.
Based on reports here, unlikely to be related to the update or with bonjour – as there are no reports of data loss like this related to the update and/or bonjour. Bonjour is a networking protocol and does not delete files. And no reports of data loss related to the update. Not saying this is definitive, but this would be a first.
What has been reported here and on forums for other apps in the marketplace, for months (if not longer) is the unreliability of Apple’s cloud services (CloudKit and iCloud). Further, the files need to be “local” and not “online”. This is NOT the default setting for Apple (nor Dropbox or other major third party sync services). Why? Dunno.
This a clue. The problems you report are related to some process that takes on the power to delete files, and Apple’s sync services can and will do that if you allow it.
Please check that the machine is NOT set for “Optimise Mac Storage” in System settings. And see Apple’s advice about all this at Access and manage your files in iCloud Drive - Apple Support and probably elsewhere.
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Wouldn’t it be a bit more convenient and simpler if the person experiencing the problems described them herself? Going through an intermediary always increases the risk of miscommunication.
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Hi, here the person going through this. Everything above described by @romebot is correct. 
I was in the panic mode, so I appreciate @romebot for helping out!
Thanks! “Optimize mac storage” is not on. Files are still in the iCloud Folder, but no longer in DT. Learned my lesson–upon clearing this issue, I will move all files to local HD. How do I do that w/o messing any linkages up?
Following what @romebot said, now that I know my files are actually on iCloud, but disappearing from DT (as well as the replicants), what can I do to save many months of work? All I want is to restore my files and replicants to DT, and further, to stop indexing and bring all my files into the database from now on, so I don’t have this problem again in the future. Any advice would be appreciated.
Are the files downloaded to the Mac?
I think so. There is no “cloud” icon next to these files.
I guess it depends on what you mean by saying “linkages”. If you mean “item links” … that beyond my experience. I did find the section “Moving Indexed Items” on page 54 (Version 3.8.7) of the outstanding “DEVONthink Handbook” which might be of use. I never did that.
When I have moved index folders, I simply deleted the original index and re-indexed to the new location. But I don’t use a lot of item links. My method is for sure brute force and not necessarily recommended.
But I have to ask. Why are you indexing rather than importing? Any particular reason? Indexing needs to be understood to have continued and sustained success. I pretty much avoid indexing unless I have a particular reason to do so. Best to re-read the whole section “Indexing and the Filesystem” in the outstanding “DEVONthink Handbook” (page 53 of of Version 3.8.7).
I mean “item link” that I have embedded for example in Obsidian and second issue is the replicated file. How to get it back in groups in which were there before.
Thanks, I will read this section. I was indexing these particular files, so I can always have access to them on the phone if needed. I read before about the possible risks, but I guess I didn’t take it seriously enough.
If imported to the database, and the database is properly synced to DEVONthink ToGo on the iphone, the files will be there available in DEVONthinkToGo and also accessible via the iPhone’s Files app.
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