Welp. I tried to reproduce it (and I swear it could be reproduced when I wrote this bug report), but it looks like it’s working now? I waited a full 10 minutes and double checked on a different device, and the folder has been deleted on both.
To answer your question though, it was synced only using Obsidian Sync.
I’ve actually been having the same problem. For me its both files and folders which reappear. I have my vault synced on mac, an iPad and an iPhone. The Vault is also stored on a Microsoft Onedrive folder. Though the issues occurs regardless of whether the Onedrive App is active or not.
If I delete a folder on the mac, then when opening the app on an iDevice the folder will sometimes but not always reappear once syncing has finished.
If I delete the file or folder on the iDevice, the file/folder will always stay.