I have opened a support ticket on this, but I am posting this here in case anyone else has this problem.
J-Link v6.40
The initial attempt to debug a program on a new board failed with a misleading error: Failed to set gdb proxy.
Using Tools > Device Programming shows that the chip can be erased, but not programmed, verify fails.
The work around for now is to use the J-Link Control Panel and override the device selection to ATSAME51J19. Programming will then work correctly.
J-Link v6.40
The initial attempt to debug a program on a new board failed with a misleading error: Failed to set gdb proxy.
Using Tools > Device Programming shows that the chip can be erased, but not programmed, verify fails.
The work around for now is to use the J-Link Control Panel and override the device selection to ATSAME51J19. Programming will then work correctly.