The COM port disappearing is a failure of the 16u2 used as the serial adapter on official unos. It is very easy to damage from abuse of the power rails, even some things that don't seem obviously wrong. It's unrelated to the package that the '328p is in.
If any of the boards are clones that use a CH340G or CP2102 for the serial adapter, those are more resiliant to this kind of damage.