Yet another DEVONThink Bug/oddness

I’ve been running the file integrity option regularly to ensure I can catch lost data before I lose it completely. I am also moving items out of DEVONThink because for me it is no longer a reliable trusted data storage system.

I am now at the point that I can verify something I thought was happening, that DT reports far more files than exist in the database. I have nothing in trash and no tags so why are there only 184 files in my database yet file integrity thinks there are 404?

Screen Shot 2022-02-20 at 5.38.00 AM

Where/what are the other 220 files?

Oh and yes, I have reported the problem to support and posted on the DT forum as well.

Are there any files in the root of the database? In the “Open Databases” section of the left sidebar select the name of the database to see the files in the root. The database in the example below has five files (which is the same as that reported by the file integrity check), of which one is in a folder, the other four are in the root.

Not seeing that the root of a database can have files in it is, in my experience at the other forum, a common issue.

You could add this smart group to a database to verify the number of documents found, including the root:

Setting up the detail display for this smart group with “Path” shown, will tell you where in the database package each file can be located:

Thanks for pointing that out. The answer is yes, some but not as many as are being reported by file integrity and more interestingly, all of the ones in root were files that I had already moved and know I deleted.

You might duplicate the database (⌘D) in Finder, for safety, then back in DEVONthink use rebuild to recreate it. See if that changes the integrity count.

I’ll say, that in 11 years I’ve used DEVONthink, extensively and continually, I have always been frustrated by the tools DEVONtechnologies provides to report on the integrity and content of databases. And the official answers in the forums often sound like handwaving. I have no doubt there are technical answers to your questions, but I unfortunately doubt the official answers will ever be 100% satisfying.

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Well this is “interesting”. Yes the integrity count changed but there are now a bunch of duplicated files in both the top level of the database and within groups!

It went from bad to worse.

Yes, I have rolled back to the backup I just made but the entire thing is really frustrating.

Could it be ‘seeing’ the files in the system Trash? i.e. using UUIDs(?) to link to files, which are found whether in the Trash or elsewhere?

Shorter question: if you empty DT’s trash and the system trash does the count change?


This behaviour also kinda happens in reverse: I have deleted indexed files in DEVONthink (ie moved them to DEVONthink’s trash), so they stop showing in the database, but they still exist on the file system, leading to some inconsistencies.

Yes. “Check file integrity” includes indexed files as being in the database even though they are not physically inside the database package. If an indexed file is deleted from the database but the trash is not emptied, then “check file integrity” will still count the deleted indexed file(s) as being in the database. The “Trash” folder of a database is part of the database, from DEVONthink’s perspective.

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no changes

the file integrity stuff is still reporting more files than exist in the database and all the root ones are gone.

Let us know what the developer’s support reports.

Would be interested too. I’m a heavy DT user and this is rather concerning.

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I live in Atlanta, so we have 404s all the time :slightly_smiling_face:

(it’s an area code here)


Could it be hidden files then?
That’s about all I’ve got.

Are you able to post a screenshot of the statistics from Database Properties?

Today’s update:

Rolled back to the backup and cleared out all the files from the root level. These were ALL files that I had already converted and deleted, or so I thought. Tried the backup, rebuild again. This time I got all the same duplicates back but at least the files I had deleted were still gone. Deleted the duplicated files and have been working with that database moving everything out of DEVONThink, deleting the files in DT, then after a time machine backup, emptying the trashes in DT and in Finder. I am continuing this process and as soon as I’ve moved and converted everything I will delete the database. This is a database of all imported files, nothing is indexed in this particular database.


I’m glad it’s working out. I don’t understand the differences in counts, or the duplicates, but I assume DEVONthink doesn’t know either. Too bad.

FWIW, I find the simplest way to exit a database is to select the database in the Open Databases section of the left sidebar, then select all the groups and root files in the file list, and use File > Export Files and Folders. Creates a new folder hierarchy in a destination in the file system.

I’m also using this as an opportunity to fine tune filenames and clean up the data and the extra steps in finder almost double the time required.

Can’t you just export everything into a folder and sort it from there? Seems like whatever is going on with your install of DT, you need to get everything out now.

I had hoped I could limp along and avoid the extra work but you’re right, I just need to get my data out safely ASAP.


This is disappointing. Exactly why I moved on from Devonthink. Sorry you’re having to deal with that…

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