I wrote this on the issue, but I’ll repeat it here…
How to solve that problem? Delete those duplicated directories and then repeat the sync? Would a simple “rclone purge” on each one of them (on the remote side, of course) suffice?
If you try the latest beta you’ll find that rclone dedupe now merges identical directories. Try it with --dry-run first as it is new code!
I understand that Google Drive produces these duplicated directories “semi expontaneously”
Yes it seems to be random. I suspect some sort of not up to date caching in drive.
Running rclone dedupe --dry-run will detect them also quite well.