Situation: I’m using Obsidian for note-taking, and I’ve indexed my Obsidian folder in DEVONthink. In order to sync Obsidian across my devices, that folder is in my iCloud drive.
Problem: After I delete or rename a file in Obsidian, DEVONthink creates a new, empty file with the old/deleted name.
I’ve seen a few other folks express this issue, but I haven’t seen a solution. Is there an easy fix? Perhaps one that doesn’t require a script, or at least a script a noob like me could implement? Or is this, perhaps, an issue with indexing in general that needs to get solved on the back-end by DEVONtechnologies?
My current solution is: I stopped indexing the obsidian folder, which is a shame because I love DEVONthink.
The behavior the OP reports is not normal, nor have I personally experienced it, but sometimes Obsidian doesn’t behave normally. I suggest creating a small test vault, without any community plugins but with the same settings for Core Plugins as your working vault. Index the test vault in DEVONthink and see if you can reproduce the error. If no, that will indicate the error is probably in Obsidian, and possibly with a community plugin.
In your production vault you can turn off plugins and then turn them on until the problem reoccurs. I know there are cases, e.g., the “File Tree Alternative” community plugin, which have settings for trashed documents that can vary from the setting in the “Files and Links” core plugin.
(Also, though it’s not cheap, Obsidian Sync service is able to manage trashes across all devices. Just saying.)
If I create a new item in Obsidian (stored on iCloud, using only that for sync), and then delete that item in Obsidian, DT still shows the item. The DT log shows it as a “Missing File.” The vault is only indexed in a single database.
As Korm suggested, I do have some community plugins. Disabling those, restarting both Obsidian and DT3, did not resolve the issue.
I am actually having the same issue (I assume) with an indexed folder that is synced (and shared) via google drive…it might be slightly different as in my case other parties (that I have shared the folder on google drive with) can obviously make changes to the folder as well.
these (from DT’s perspective) missing files then create issues when doing a bonjour sync between DT and DT to go until I manually remove them…
That’s definitely not a DEVONthink issue; it’s a personnel problem
It is best to have tight controls over such a resource. If you are indexing such a group, people should not be allowed to remove files from it (or potentially add or rename either). If this is your folder on Google Drive, I would administer it much more carefully to avoid missing files in your database.
Thanks for the great suggestion, @korm I just tried out indexing a new test vault.
As @BLUEFROG correctly noted, renaming is not an issue. DEVONthink is (impressively) quick at updating names of files. Sorry for my confusion there.
(To @BLUEFROG 's other questions: I’m using a macbook, imac, and iphone all with both obsidian and DT. I’m indexing the vault only in a single database. If it matters: I’m using iCloud (cloudkit) to sync DT plus iCloud drive to sync Obsidian.)
I’m having trouble reliably reproducing issues. Some things that have been happening:
I delete a file from Finder directly, it’s removed from DEVONthink.
I delete a file in Obsidian, it persists as “File missing: path.” I try “Updated Indexed Items” but it’s not fixed. Later, I check DEVONthink and it is fixed.
I delete a file in Obsidian, but do so very quickly after it shows up in DEVONthink, and then it is immediately removed from DEVONthink. (I wonder if this means something is going on with sync?)
After turning of community plugins, but not core plugins… I index the vault in DEVONthink. I create a new file in Obsidian. DEVONthink doesn’t notice that new file. I try “Updated Indexed Items” but it doesn’t change. I index the vault again, now it does notice the file.
I’ll keep experimenting to see if I can more reliably pinpoint the problem and cause.
If your files are in iCloud, there’s a possibility that iCloud is one, if not the sole, culprit. iCloud is notorious for having synchronization problems. Check out Howard Oakley’s advice.
(Personally, my vaults are never on cloud services, residing in ~/Documents. My vaults used to be on iCloud, and these mysterious “missing files” issues were common. Since moving everything to Documents, the problem never occurs for me. I use Obsidian Sync, but there are other low-cost/no-cost optoins. See the Obsidian sub-Reddit for extensive discussions of options.)
If your delay with DevonThink occurs for files that have been around for a while and not for files that were only created a few moments earlier, that would suggest the problem is with iCloud (the newly created file wouldn’t have synced to iCloud yet, but one that’s been around a while won’t be disappearing immediately from iCloud when you delete it in Obsidian).
FYI: I’ve successfully indexed my Obsidian vault in DEVONthink using Obsidian Sync to get files across my devices. I’ve been running this way for long time. My Obisidian vault is not in my iCloud system. Good luck with your setup.
