Synced SharePoint files return after being deleted

We had that happen a while ago and it was a nightmare. Someone would delete a file and then someone else's computer would add the files back to the site rather than delete the local copies. By looking on the site we could see who was doing it. I think we had to uninstall the client from that person's computer, reinstall and start syncing again. But sooner or later it would happen again with someone. We finally had to stop people from syncing. 

However, I thought it had to do with the old client. I haven't seen the issue since we upgraded to the new OneDrive client. Are you sure you don't still have someone using the old one? Maybe find out whose computer is adding the files back in and check their OneDrive version.