I believe the issue here is there is only a single clock that feeds all three CAN modules (SC_R_CAN_0), in the SDK when you call -
/* Power on Peripherals. */
if (sc_pm_set_resource_power_mode(ipc, SC_R_CAN_0, SC_PM_PW_MODE_ON) != SC_ERR_NONE)
{
PRINTF("Error: Failed to power on FLEXCAN\r\n");
}
This will enable the clock as well, but if you use SC_R_CAN_1, I don't believe the clock will get enabled, which also explains why when you initialize CAN_0, CAN_1 then works.
The fix is calling the above for both SC_R_CAN_0 and SC_R_CAN_1 should work, in order to use any of the CAN modules a call to CAN_0 will be needed.