In practically all companies that produce electronics with flashable firmware, the first thing they check is the FW memory, if anything not made by them was flashed. Nintendo most likely is the same.
So, if you want to send it to them under Warranty, they will send it back with a memo that by modifying the device you voided your warranty.
If your warranty expired and you are going to pay for repairs, then more than likely they will reflash your whole console to be stock.
So, if you want to send it to them under Warranty, they will send it back with a memo that by modifying the device you voided your warranty.
If your warranty expired and you are going to pay for repairs, then more than likely they will reflash your whole console to be stock.