I suspect you were using chinese knock-off Arduino Pro Micro modules. The regulator on those are often marginal compared to authentic parts and will sometimes go up in smoke around 12V. You might be able to replace the regulator with a genuine part from the BOM and have no trouble. You may also put a diode in line with the 12V input to bring that voltage down a bit and protect against reverse power. Or just buy genuine assemblies from the OEM and save yourself a bit of time and frustration.