Thrustmaster knows this is an issue and chooses to not revise their PCB design. I believe, but have yet to confirm, that this is caused by the lack of ESD protection on the D+/D- lines for the USB. In my discussion with TM support, I asked for more details around the root cause, but they were not willing to share. This thread seems to provide ample evidence that this is a serious and recurring issue. These are not cheap input devices and shouldn't be damaged by simply plugging into the wrong USB port at the wrong time.
In an effort to properly address this problem, I have designed a board from scratch for the Warthog Throttle that should be a drop-in replacement, but with minor improvements (ESD protection, etc). I'd like to test this with the official TM firmware, but don't have a proper hex with bootloader and app. If anyone out there who has been dealing with this same issue has the full fw image and wants to collaborate to solve this once and for all, message me. I would be happy to share board files and eventually, once properly tested, provide all information to TM to hopefully get the changes into their product(s).