Hi @FredrikMoller
MIMXRT1170-EVK can work with the external JLINK debugger, I have tested it on my side previously.
Please follow me to test it again:
1. Board is powered using 5V wall power at J43, J38 connect 1-2.
2. remove J5,J6,J7,J8, it will disconnect the on board debugger.
3. Connect your Segger JLINK debugger to the J1
4. Use the JLINK commander connect the board:

Wish it helps you!
Best Regards,
Kerry