Hi,
It sounds like a bit of a mess there! Should be pretty straightforward to clean up, but might be rather time consuming if it becomes necessary to go machine by machine. I'd love an opportunity to discuss the issue with you further and determine the best resolution and perhaps improve processes to ensure that the issue doesn't return in the future.
I manage both a large heterogeneous hosting environment across multiple sites as well as dozens of varied onsite client virtual environments. I've dealt with similar issues before, so this should be very much solvable.
Thanks!