I have a few separate iCloud folders indexed in a single DEVONthink database. I was working with one of them (“Quigley”), dragging a few documents into the database and copying others out. All of a sudden, files from a completely different indexed folder (“Finance”) started to disappear from a Finder window.
I soon figured out that many files were moved from “Finance” into “Quigley”. It wasn’t user error, accidentally dragging something from one place to another. Many files within the structure of “Finance”, at various locations and depths, were not moved.
I quit DEVONthink and moved everything back using Finder. When I restarted DEVONthink and asked it to update the indexed files in the database, “Finance” was removed from the list of indexed folders once the update completed. There is nothing in DEVONthink’s trash to suggest I deleted it. Also, “Quigley” shows in DEVONthink with a subfolder that’s not visible in Finder or using “ls -a” in the shell. The documents in the phantom folder within “Quigley” show with a cloud icon to the left of the icon that indicates a linked file.
I’ve not yet added “Finance” back as an indexed folder or tried any other modifications. The database verified successfully.
I’d like to figure out what happened, a post-mortem of the event. Are there particular steps I can follow, like reviewing particular DEVONthink logs? I’d also like to figure out what is broken with the database now and how I should go about fixing it.
No worries! There are just a lot of variables that could come into play and so far what you’re reporting doesn’t sound like anything inherent or normal.
Is Quigley a subfolder of the Finance folder in the Finder?
And do you use any smart rules or other automations? Do the indexed files/folders have any Finder tags and is the option to exclude groups from tagging, see File > Database Properties, disabled?
I do have some smart rules that are set to on demand. I haven’t run them in at least a year.
The database property, exclude groups from tagging, is enabled.
There are no Finder tags in either folder.
The incident involved folders I was working with at that moment in DEVONthink. But, I will say that the folders are shared iCloud folders. No other computer was working with these files at the time. And the location changes of files were too random and extensive to be intentional.
I will also keep eyes on this, as I am still searching gor a) an explanation and b) a solution myself 
