Holyshit dude you're scaring me. I wasn't particularly gentle with taking off the crusted cement like thermal paste either ... now I need to get them online and check them asap.
Generally when the GPUs are new, you can easily take off the GPU from the heatsink because the paste isn't hardened like glue. However on an old GPU that was mined for a few years usually the 2 parts are stuck on.
I noticed I got issues only when I turned off the rigs to clean them, they mined fine for a few months, I just down to clean and it was when I powered the rig back up, it wouldn't boot and after inspection turns out one GPU basically went directly into BSOD during boot-up. I had a few GPUs do this and all of them had a thermal repaste job.