Dealing with orphaned files & duplicates


Apologies for posting what I expect is something that has been answered many times before, however I have not been able to find a clear answer as yet.

I have two problems

1) Orphaned files
After performing a database verify and repair I was left with 766 orphaned files (these where placed into an orphaned file group). I have found that every file that I have looked at so far which is orphaned also appears in my file listing in my database. So question is, how can it be orphaned if it also appears in the database file list (i.e. DevonThink knows about it)? Secondly, where this is the case, what am I to do with the file placed in the Orphaned file group? Is it safe to delete?

2) Duplicates
I have a heap of files which are marked as duplicates (partly due to the above problem). However if I use a duplicates smart group and sort all the files by name there are many files which do not have a copy of themselves immediately below or above it… so I have no way of knowing which other file DevonThink believes it is a duplicate of. If I do a Data -> See Also & Classify, no other files appear in the list. So how do I find out which file DevonThink believes it is a duplicate of, and secondly if it turns out it is not a legitimate duplicate, how do I tell DevonThink to not mark it as a duplicate?

Thanks & Regards



Just because a file exists in a database, it doesn’t mean there can’t be an orphaned file in the internals. Depending on what processes, scripts, Hazel rules, habits, etc. may be in play, orphans are created by adding files to the internals of a database, outside DEVONthink’s knowledge. In fact, people often get into this situation by doing a Save As and not paying attention to where the new file is being saved.

A duplicate is not necessarily a copy of a file. See: … evonthink/
You can’t tell DEVONthink to not mark something as a duplicate. In the case of images or files with no text layer, the thumbnail can be used to determine a duplicate status.

Thanks for the response.

So if I have a file, e.g. xyz.pdf in the orphaned file group (created during the database verify and repair), and I also have file xyz.pdf in my main database file list (in my case, sitting under “Mobile Sync”) is the copy in my main database file list “un-orphaned” (after the database verify & repair) and I can delete the copy in the orphaned file group? If not, what am I supposed to do with it?

As for the duplicates, I read the article you linked to below previously. So I understand if I have document xyz.pdf marked as a duplicate, there does not have to be another xyz.pdf for it to be a duplicate. My problem is what I don’t know or can’t tell which file is the duplicate pair. Surely there is some way that Devonthink can tell me which other file it believes is it’s duplicate (otherwise it could not mark it as a duplicate). I thought that Data -> See Also & Classify could tell me that… but apparently not. If there is no way, there is no way



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If you have determined it’s just an extra copy, sure you can delete it.

As a side note, the Mobile Sync group has no function for syncing any longer. In fact, it is no longer present in newly created databases. You can still use it, but I wanted you to be aware of this.


See Also actually will show duplicates, but check out the Instances dropdown in Tools > Get Info for a list of duplicates.

I am more confused than when I started reading this thread.

So, based on what @BLUEFROG said, there is no safe way for DT to scan an inbox for duplicates, and then delete the duplicates?

The previous responses were four years ago and related to DEVONthink 2.x.

In DEVONthink 3, there is a built-in Filter Duplicates smart rule in the Navigate sidebar that can be activated, targeted to the Global Inbox, and will move duplicate files to the Trash. However, make sure you have Preferences > General > General > Stricter recognition of duplicates enabled first.