Since the schematic says "multilink" on it, and it shows Port B, good chance that's the tool he is using.
That's pin 15 of the P&E Connector. It goes to pin 34 of the MCU, according to the schematic, which as I said looks correct.
If you look at the tech ref of the Multuilink Universal, you will see that Port B, "Kinetis" pin 15 is indeed reset.
I have personally never had a problem with a P&E un-securing a device, bit I suppose it could happen.
He has no control of the RST as the P&E BDM drives that low, so you will have to explain what you mean by "make sure you keep it low".
Again, recommend you contact P&E tech support.