Hi,
Debugger is not available while BKGDPE is 0. You need to debug required pin function perhaps on another pin, on device having spare pins, or just being careful about coding. For debugging the rest of your code you need to use some define to avoid clearing BKGDPE. Yes, it's not very comfortable, but you win extra output pin. On S12 devices there's a MODE register, which helps detecting are you using debugger or not. I don't see such feature on QE8, you need to recompile you code for debug with BKGDPE=1.
BTW you should not load BKGD pin with external pull down load. On power up until you clear BKGDPE this pin still functions as MS/BKGD. Having it pulled low MCU won't start and keep waiting for BDM commands.
Edward
Edit: fixed BKGDPE, 0 - GPO, 1 - BKGD