Hello, nice to hear that you keep regular backups! Please keep doing that, especially before such operations.
I imagine there are 3 things that can happen if you point a device synced with outdated cloud to your live unsuspecting sync target. If the outdated cloud haven't been changed since you stopped using it in the past, you'll get completely normal merge, no conflict, just a new version of your notes.
If there are small changes, you'll most likely get conflicts which needed to be sorted manually. There's a possibility that entire note base with thousands of notes would be marked as conflicts.
If the changes are large, Joplin might think that your outdated cloud is new cloud and will mercilessly delete all the up to date notes on the live cloud and replace it with outdated versions.
Problem is you might not know if outdated cloud was changed automatically for some reason (by server, OS or any other means). Even update in modification date might be a deal breaker.
In your case, I'd just wipe the device which was synced to outdated cloud and set up the correct target. But if you like to live dangerously , backup well, set off some time to fix conflicts and let us know how it went
Just wiping the offending device would be the simplest answer, but my problem is that I was using both “branches” and both have data I want to keep.
To oversimplify, I have a desktop connected to Joplin Cloud, and an iPhone connected to Dropbox. I want to get all of the new notes I made on the iPhone into Joplin cloud, but not duplicate all the notes that were in Dropbox before the migration from Dropbox to Joplin Cloud.
I also forgot. One other thing that may complicate everything is that I turned on E2E when I migrated.
In that case I'd suggest testing the merge by uploading Joplin Cloud data to other cloud, say OneDrive and then pointing the outdated iPhone to that new cloud as well. It's going to take a while but I think it's the safest approach in your situation.
If things go well, you can restore to current situation and merge with your live Joplin Cloud. If not, the damage wouldn't be irreversible.
There are a few tools that might help you with eventual conflicts: