Don't wast time pulling fuses for minutes, unplug both and as soon as you plug in you are fine and it resets the PCM to read (normal) mode. You then flash away.
I don't have HPT, so I don't know how it works, my tuner if I know I have a corrupted cal, I check off PCM Recovery, if I am changing OS, then I do a full flash. Easy...
edit: how do I know on this? 1, work in the electronics industry, so I play with parts like this, 2, I have done it so many times it isn't funny. My Buick has the memory seat option, which is cool, but if you touch ANYTHING (radio, seats, climate control, etc) while the car is being flashed, it hangs the PCM in flash mode. Then I have to pull PCM fuses and start over keeping my paws off.