Please HELP! DT3 most likely causing me to delete files on my disk

I started using DT3 quite extensively for its great features, about two months ago.
Unfortunately, it is DT3 that is most likely causing me to delete files on my disk (probably some optimization and automation set by me) and what is worst is that this is secondarily transferred to the sync with DROPBOX where my work files are also deleted.

I have suspected DT3 since Friday last week when I first noticed this situation.
As a precautionary action I have:

  • started using DT3 on a limited basis,
  • started looking for other applications that could be causing this - such as TIME CAPSULE and other backup - file transfers within my backup processes.

By following the procedure described above (and thanks to DROPBOX, which allows to recover deleted files), I have reached a more or less stable state, as I have been used to on MAC OS for at least 10 years.

Tonight (CET) I needed to work with DT3 for approx. 1 hour (after upgrading to DT version 3.8.4) and again files were deleted that synchronize with DROPBOX (and disappear from my disk), thus disrupting the whole WF as I had to :

  1. first restore from DELETE state on DROPBOX
  2. synchronize DROPBOX with my iMAC
  3. and start working on my standard work files again

So far all my attempts to identify and interrupt the source of the above described problem have failed.

I am running macOS Monterey 12.4 iMAC with 32GB RAM and 2TB disk. As an office application I use Office365 Excel, Word etc.

Is there anyone here who is able to advise me what to do in a situation that has been burdening me for almost a week already?

Never had anything remotely like that happen. Are the disappearing files in a folder you’ve added as an indexed location? If the files aren’t in an indexed folder, it seems unlikely DT is the culprit.

If you delete an indexed folder or file in DT, you can safely empty the trash if you choose the “only in database” option.

You can get a roster of all the files in your DT database by expanding all your groups, selecting everything, and then use Tools->Create Metadata Overview.

Hope you find what’s happening.

Hello, thank you for the tip on how to look into this.

As part of a quick look (I’ll have to continue more tonight CET) it looks like you can assign files from DT to directories that disappear under the scenario described above.

The random character on the DROPBOX was also striking, and it’s my first clue as to what might be going on. The same directories keep disappearing from one/many subdirectories/subdirectories (example: a subdirectory with 2022 projects and from this subdirectory some disappear fine, but they keep repeating).

I’ll be able to look at this in more detail later or over the weekend.

But if suspicions are confirmed, what would you recommend to do next?

Namely, what I saw in the quick view is the first clue to what is happening with deleted directories containing files from DT.

Best regards

Welcome @VLKa

I’m also guessing you’re indexing files.

  • Have you read the Help > DEVONthink 3 Help > Documentation > In & Out > Importing & Indexing section?
  • Are you using Dropbox’s Smart Sync feature where you files are stored on their servers?
    • if so, you should not index these files. You should index locally available files.

Do you have any second Windows/Mac suspended with same Dropbox synchronized files?

Hi BlueFrog,
thank you for your interest in helping me!

Regarding your query, I only started reading this linked document today, my thoughts were based on the original DT3 version 3 documentation that I purchased with the product (as part of the DT3 license, or when moving from DT2; I only used DT2 occasionally, as part of testing, and preferred Evernote and Zotero due to its complexity).

Given the amount of text and studies that are the subject of my professional activity, I have reverted to the DT version 3 product based on reviews and evaluation of various recommendations aimed at improving WF for “writers”.

I have attempted to incorporate this product into WF based on reading the original manual that I purchased with the upgrade to DT3.

It was definitely a good decision (at least in theory), because the way Evernote has been going for the last few years (but not erasing files from my disk; even in theory; yet :-)), I don’t like it.

I definitely use indexing, not just files, but entire subdirectories (those will probably disappear).

I’ve also read that the optimal thing to do is to do it on “local” files, i.e., as I understand it, those stored on the local drive, which is (probably) my example, with those local files being transferred to the cloud by another paid sw (dropbox) (and at least in theory staying the same, unless you change them from a MAC laptop while working on the road; but here the change is cool… )

This is probably where I made the biggest mistake, because according to DT (?) these are not “local files” (I don’t want to get into the “bypassing the MAC Monterey file system” by Dropbox here), but the fact remains that all WFs worked for me until I switched to Monterey after testing at the end of Q1 this year.

To answer your other question, I use DROPBOX’s Smart Sync feature in that it cannot be removed from their client, but it is set as “Available Offline” on the iMAC station.

Otherwise, I use DROPBOX’s sync to sync DT3 dB (which are located on the iMAC’s disk somewhere other than my “DROPBOX work files”), while the other options from the DT3 menu don’t suit me.

I won’t bore you with a long description of the situation, my partial working conclusion is that I’ve gone overboard with the indexing and automation logic, and the question is whether you can advise me how:

  1. leave the files in the DT3 db, but
  2. how to gracefully undo the indexing and
  3. so try to fix some received state.

Only after resolving this awkward situation with “disappearing files” can I address the question of my further education around “DT3 knowledge”. The only reason for this approach is that I am currently very busy at work and this state of my iMac is certainly not conducive to peace of mind at work.

Do you have any ideas on how to do this gracefully please?

Thank you for your help and I would be glad to hear from you.


Hey, rfog,
I have a Mac as a second laptop, but it is not suitable for such DROPBOX testing (btw: I tried to solve such a situation with DROPBOX help as a first line solution; we solved slightly different problems with them). I’m only waiting 2 months for a new laptop (with M1 processors) from Apple :-); the good news is that delivery will be done by July 15 (probably).

That’s not a good and fast way, which I prefer now.

Thank you very much for trying to help me solve my problem!



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Hold the Option key and choose Help > Report bug to start a support ticket.

I was asking you if you have a second Mac with DT installed and suspended.

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Yes I have a second MAC where DT3 is installed and suspended. I only use this one on the road to have mobile access. This NB has not been turned on since I diagnosed the file disappearance problem.
Thank you for your help, I didn’t mean to be rude.


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I will try this method and I will inform the community with the result.
Thank you for your help.


You’re welcome :slight_smile:

I had something similar happening to me.

In DT I had indexed a folder of text files that was under Dropbox. Then files started disappearing, especially right after they have been modified and closed (they were moved to the trash).
I removed the indexed folder from DT, but for some reason its content kept reappearing (I have contacted supported at that point and didn’t quite have a clue of what I was talking about, a indexed folder reappearing). For a while I thought the problem was somewhere else, I moved the files out of dropbox into another sync service (and did not index them in DT) and stopped having issues.

At one point it dawned on me that the various replicas (one more PC, an iPad and an iPhone) may be recreating the indexed folder - so I deleted the folder in each one of the replicas - synced them… and the indexed folder was no more. I moved back to use dropbox and lo and behold, no more deleted files in my dropbox folder.

I will never know what it was that hit me, but I will just refrain from indexing dropbox folders in the future.