Start with a setup like this with both the originating PC and the peer being Windows 10 PCS:
---- "Test" folder with files in it.
------An "Under Test" subfolder (with files in it) under the "Test" folder.
Let this be synced with a peer.
Rename "Test" folder to "test".
Let the rename sync the change (all is good)
Rename "test" folder back to "Test"
Consistently the "Under Test" subfolder and it's file are deleted on both the originating PC and the peer.
So changing case on a folder (not the sync folder, but a folder under the sync folder) back and forth between upper and lower case will delete any folders underneath it along with the files within those lower subfolders.
I've been able to reproduce this consistently. I understand that it is challenging to handle case sensitive renames, this kind of thing breaks SyncThing too, although I couldn't get OneDrive to break in this way. This might seem like a rare situation, it is not so far fetched. I stumbled on it when I renamed a folder to upper case, and then later changed my mind and renamed it back to lower case... these kinds of things can happen. It wouldn't be so bad if RS created two folders, but it deletes folders underneath the renamed folder..that's dangerous. I suspect that since individual files in the renamed folder have specific HASH identifications they are kept, but subfolders don't have that, so they and their contents are lost. I replicated this with both the stable 2.5 release, as well as the latest 2.6 bets release candidate.
This should be easy for one of your programmers to replicate.
I love RS a lot, but this is a problem for me until it's fixed.