In my case, I would have made a snapshot of the VM image before installing the SEPM software. Once installed, set it up. And I would have used some test PCs for testing purpose where you're happy to trash/rebuild when completed.
Once you're happy with it, you can either keep as it is, or roll back the VM image where needs and rebuild these PCs for a fresh set of PCs for fuerther testing.
This way, it would be a lot less hassle for you to deal with this.