I’ll try to elaborate, as I spent my last weekend refining my system for this (and yes, I know how that sounds).
I keep all my notes in Markdown .md files. Last week I hit a bit of a break in deadlines and got tired of having notes in Agenda, Ulysses, and loose files, so I decided to consolidate. I wanted my files to (1) be next to other relevant files in project-based folders; (2) to be free from proprietary lock-in, and (3) to be able to be automated using AppleScript, Hazel, DT3, and Shortcuts as necessary.
So I don’t want to leave things in DT tools. With Indexing, I point DT3 at a folder and it represents each file in that folder in DT3. If I use a cloud-based storage provider’s folder for this, the file is synced and can be edited in three places: the desktop filesystem, the cloud storage provider (e.g., dropbox.com), and inside DT3.
In general, things sync so quickly between these three places that the file is figuratively edited in all three places simultaneously. If I make a change on the file system, DT3 recognizes and updates its representation of the indexed file, and the cloud storage app syncs the change up to the cloud. Vice versa for any other direction of sync.
On iOS, however, DEVONthink To Go (DTTG; DEVONtechnologies’ iOS app) does not index the iPhone/iPad’s filesystem. It syncs DT3’s representation of the indexed files. A file synced via another cloud storage provider is a representation of the desktop filesystem’s version of the indexed file. So if I open-in a Dropbox file that is also indexed by DT3, DTTG has no way of noticing that update from DT3 until your Mac picks up the change, updates the indexed file, and syncs that to DTTG. This is the round trip.
If you edit an indexed file in DTTG it works the same way. Gotta sync it to DT3 before the change will be represented on the desktop filesystem or in the cloud.
It sounds awful, but it isn’t. I have yet to observe a conflict, perhaps because I’m a little careful. It should get better as more apps use iOS’ Files to enable “Open in…” features with DTTG as a file provider.
An unnecessary but perhaps informative detour: I adopted iA Writer as my “core” Markdown editor because it can edit files in-place. In fact, it has a nifty Library Locations feature on iOS that allows you to point it at a given file directory for in-place file creation, opening, and syncing. Unfortunately, this only fully works with iCloud, Working Copy (iOS), and a few other providers—no Dropbox. So I moved all of my files to iCloud /documents and have been fine with that. (No big collaboration needs yet…) So, If I’m writing on iOS I open iA Writer and edit from there.