First, I would not post a question like this in official Q&A… but pretty sure the community will give you a ton of knowledge on PTCs.
Usually illegal teams cut off the PTC and hook up the two ends with wire. The motor runs normally, but it can overheat and melt/burn the shell and anything, which is why it is illegal – unfair advantage and violation of safety, and of course, it is cheating.
I doubt that cutting off PTC will burn the cortex. Motors have their own PTCs, and so does the cortex. Port 1-5 and port 6-10 have their own protections, and the cortex will shut down under too much current. Plus, power expander has PTC in it too. There is not a easy way to burn down a cortex with a mistake, I think.
However, cutting off motor PTC absolutely can burn your motor shell very nicely. Never do that if you want to compete.
A 393 without PTC will destroy itself in about 5 minutes (so I hear, never tried) if connected directly to a battery and stalled. The PTC inside the cortex should stop this happening if the motor is connected to it, trip time for that one is somewhere between 15 and 60 seconds with motor stall current of ~4.5A (see data here PTC performance measurements)
Bypassing the PTCs in the cortex would probably result in damage to the motor port connector on the cortex but the actual CPU would probably survive.
So to answer your question, I doubt an illegally modified motor would “burn up” a cortex.