I’ve had no problem for years.

Biggest issue I’ve had was forgetting I committed something on one device before committing on another. Then I had two branches where one had " conflict" in the name. I just deleted all conflict files and everything continued as normal. If your repo is never corrupted before syncing worst case you should be able to find and delete all conflict files.

Syncthing conflicts include the source of the conflict so you could just choose to delete all files whose conflict is from one device and leave everything from the other.