Looking at the circuit diagram, there is a SAMD11 between the USB connector and the MG24’s SWDIO/SWCLK, which appears to be performing some kind of interface function.
On the other hand, since the MG24’s SWDIO/SWCLK pins are exposed on the back side, I believe it should be possible to upload a new sketch using an expansion board and JLink.
However, since the CMSIS-DAP connected to the USB port is reporting that the IDR is not visible, I suspect the issue lies either with the SAMD11 or that the MG24 is refusing to cooperate.
By the way, can the lock bit be easily verified using JLink?
EDIT:
It seems that JLink can be used to access internal registers and memory, so I will give it a try.