I have been using Devonthink for 10 years to research projects. I am using a Mac Studio desktop computer with Time Machine backup and offiste Crashplan. I recently started a new research project on May 25, 2025. I have a dedicated database just for this one project, with about a dozen folders and half a dozen subfolders. I had to restart my computer one day ago because of a hardware issue (wired mouse). When I tried to save to this project today, nearly all the stored file had been moved from their folders and designated orphan files. I then tried to follow the prescribed solution, closing DEVONthink and copying the database from Time Machine to a different location. When I opened that database, only about half the folders were present. While trhe files were int he correct folders, it appeared that everything after May 30 had disappeared. I also checked my crashplan backup and it too only had files up until May 30 in the database. Oddly, some of the files after May 30 were among the orphan files listed in the existing database. But none of the folders I created after May 30 were present wither in the original database or the Time Machine backups. How can I prevent such data losses going forward?
After a quick search I have learned that offiste Crashplan is some online backup service. So my question is: What do you backup with it? The live databases or database backups? If it is the live databases I would bet that is the issue.
There’s not enough information to assess a cause.
- Are you importing or indexing files?
- How recent was the backup?
I import all the files by using print in preview and selecting save to DEVONthink and then choosing the appropriate folder or subfolder. Time Machine has regular backups – I’ve tried saved backups from before the restart and after. The most recent crashplan backup was yesterday. So my conclusion is that everything I saved in the database after 5/30 was considered an orphan file even though when I opened Devonthink it showed them in the correct place as recently as yesterday. But the Time Machine backups didn’t show them at all.
Like time machine, crashplan makes a passive backup every couple of hours of the entire home folder.
Where are you saving the files to?
What folder and subfolder?
I have a database named Sage in my Devonthink database folder in my documents folder. It has folders for research projects for this company. I have a subfolder called US-China. In this folder are 10 subfolders. Within these subfolders are five subfolders. I save the printed article to the folder appropriate for my research. The main question is: why did Devnothink stop storing these properly more than two weeks ago? As of Monday, everything looked correct in the proper folders. When I restarted the computer all the files that I had saved since May 30 were made into orphan files. Luckily, they are still there and I can redistribute them. But what I need to know is why would they be orphan files if they showed as being in the proper folder originally? I don’t want this to keep happening.
Just my opinion but I would never put my databases in my Documents folder. It feels dangerous to me.
The main question is: why did Devnothink stop storing these properly more than two weeks ago?
After you print to PDF, are you choosing a group in DEVONthink’s group selector?
The Documents directory isn’t inherently dangerous. However…
- If people aren’t paying attention, they could have enabled macOS’ disk management via iCloud Drive when setting up their Mac. That would not be a good thing.
- If people get the idea they need to use said disk management, they don’t stop and think, “Wait… aren’t my databases in the Documents folder?? I should look and move them.”
That’s when problems could occur. Fortunately, DEVONthink has had a mechanism to detect when a database is opened from a dangerous location and disallows opening it. This situation is a big part of why DEVONthink 3+ creates the safe Databases folder and treat it as the default save location when creating or importing databases via sync.
Ja, Bitte verzeihen Sie mir, dass ich die falsche Terminologie verwendet habe. I should have said group when I wrote folders. I save pdf to devothink, then use the group selector to determine where the file is stored.
Well, what changed two weeks ago?
When something that was working fine suddenly stops, usually either one of the pieces of software involved had an update that changed its behavior, or the user (knowingly or not) changed a relevant setting.
I have store desktop and documents in icloud turned off.
Either we’re missing some detail or you’re reporting very unusual behavior.
In DEVONthink, hold the Option key and choose Help > Report bug to start a support ticket.
You have expertly summarised why I feel that putting databases in the Documents folder is somewhat dangerous
This is an interesting topic. I have created a master vault folder in documents which contains all databases and a lot of data that has been imported to DT. iCloud has been turned. I have a script that closes DT at 05:00 everyday and I then backup my master vault to a synology NAS at 05:30. I have a WebDAV sync to an external storage service and Time Machine on my synology NAS. My NAS is backed up to an external HD.
I also manually copy local copies of my Databases to a backup folder in my vault.
I am concerned about the comments that the document folder is unsafe. Why. Is there a recommended backup strategy published.
I disagree that a sub folder under ~/Documents is unsafe. I use it.
What is “unsafe” in my opinion is using Apple’s “optimise disk space with iCloud” (or what ever they call it these days) where the macOS will “help” you by moving files off your computer to iCloud. To save space or something. It does that to ~/Documents and other folders.
DEVONthink expects all files to be local and available. Not deleted and/or waiting for iCloud to bring back the deleted files. No telling when iCloud will get around doing that.
I could maybe quibble with your backup regime eg i would suggest making database archives . But if it works for you, great. Have you tested, once and at intervals, you can restore?