I was having the same issue only none of the Print Management / removal / deletion / registry deletes from HKLM\System\ControlSet001\Enum\SWD\PRINTENUM & HKLM\System\CurrentControlSet\Enum\SWD\PRINTENUM, HKEY_CURRENT_USER\Printers\Connection and HKEY_USERS.DEFAULT\Printers worked. I tried all of the following:
Empty the spooler folder: When a deleted printer keeps reappearing, it could be because there are still jobs associated with that printer are still in the spooler and can't be flushed. In Server 2012 R2 and previous versions, you'll want to check the following path: C:\WINDOWS\system32\spool\PRINTERS. There you'll see spool files with .shd and .shl extensions. Delete all of the files it contains, then restart the spooler service.
Delete the driver: On rare occasions, a driver will be associated with a particular printing device and cause it to persist. In the event that a printer cannot be removed because access is denied in Server 2012 R2, try deleting the driver. This can cause a lot of problems if other clients are still using that driver, so be sure to do it during a quiet period. Reboot the server and see if the ghost printer is gone. If so, you can safely reinstall the driver. Try upgrading to a newer version if the previous one was outdated.
Play the printer spooler game: Sometimes removing the printer can require a little added dexterity on your part. Some admins have reported that they have had to stop the spooler, then start it, and then immediately attempt to delete the printer via the Print Management console before the spooler has finished starting. It might take a few tries.
Check for stray registry keys and redirects: If you're finding that a ghost printer cannot be removed because access is denied in Server 2012 R2, there's a chance that it is still in the registry. Lingering registry keys can prevent a printer from being deleted. To remove a printer from the registry in Windows Server 2012 R2, try scanning the registry keys and running a repair process with a software tool.
I had 42 printers, mostly 4 to 5 copies of the same printer, and no matter what I tried they would just keep coming back. In the end, in desperation just before I was about to rebuild the machine, I tried CCleaner's registry clean (there are probably better ones but had this one on hand and this has fixed the issue.