Interesting. Is this on DEVONthink 3?
I think indexing has gotten a lot better in DT3, but I do notice some weird behaviours once in a while—not often enough to discern a pattern, though, and nothing has really caused me problems.
Yes on latest version 
I reached out to DT and they said
“That’s a known shortcoming to avoid data loss in case of synchronized databases containing indexed cloud folders as the deletion inside the [cloud] folder could be the result of using the command Move into database on another Mac.”
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Hm. To be fair it is a tricky thing—Indexing a cloud-based file means tasking several different services with keeping track of it (and, in a sense, competing to do so). I would recommend trying to stick to a personal protocol that avoids the errors (and backup, backup, backup). Maybe someday it’ll get better!
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I would love to read a write-up on how you’re using Obsidian and DEVONthink together. That is the only thing that I’m sort of disliking about DEVONthink is the writing experience.
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Devonthink is essential for me. I use it as a document and research repository. I put stuff in there and never take it out.
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I use Byword editor app as a crucial part of my EagleFiler workflow. Can’t you set an alternate external editor with DevonThink? It’s been awhile, but my memory is that you can. Use Byword or iAWriter, etc, instead of DT’s built-in. (I don’t even need that facility in EagleFiler – Byword by default at the macOS level opens all my plaintext files for me from within EagleFiler.)
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Devonthink allows you to open any note in a compatible editor.
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Yep. I use IA Writer currently–same app on Mac and iPad.
Much easier to use external editor on Mac DEVONthink via doubling clicking file, but need to invoke share & choose iA Writer from menu on iOS is cumbersome. Hopefully soon DEVONthink will improve its editing capabilities.
Share > iA Writer doesn’t work properly in DTTG (even the latest version). At least, it doesn’t show images for indexed files. This seems to be a limitation with the file provider protocol.
Instead you have to got to iA Writer (or other markdown editor) and then navigate into DTTG to the correct file before images will show.
Aware of issue with images with external editors thus like I mentioned in other threads hoping DEVONTech will improve markdown editor soon 
Compounded by fact that I prefer using link items for linked files and images so sticking to DEVONthink to read and follow links. iA Writer is for long writings; luckily don’t use a lot of images.
It occurred to me just now that my interminable search for a note-taking alternative to DevonThink is paralleled by the most recent episode’s discussion of Fission and Acorn as lighter-weight alternatives to Logic and PhotoShop.
DevonThink is an incredibly powerful application—but usually I just want to write something, read a document, or take notes on another document, and DevonThink is a LOT if that’s all I want to do. But sometimes I need everything DT offers.