Rule of thumb:
- Empty directory
<vault>/d/XX/YYYYYYYYYYYYYYYYYYYYYYYYYYYYYY/
is important and should not be deleted to maintain integrity of the vault. - Empty directory
<vault>/d/XX/
could be deleted but you have to make sure that the vault directory is 100% available (e.g., fully synced with a sync client if stored in a cloud storage).
In general, you shouldn’t manually rename/move/delete anything inside the vault directory (except you absolutely know what you’re doing). I just wanted to clear things up from a technical point of view.