Are you using processor expert to configure your board ?
If so, could you share your CAN configuration (pinMux, flexCAN) ?
That example is configured to work by default over UART. In order yo use CAN communication you would need to:
1. Configure CAN peripheral
2. Configure CAN pins
3. Call FLEXCAN_DRV_Init in the initDemo() function
4. Enable CAN interrupts (if you want to use FreeMASTER SHORT/LONG INTERRUPT mode)
5. Update freemaster_cfg.h to use CAN instead of UART
I commented the battery setup (I can not test a e2e scenario as I don't have a corresponding setup) and added the CAN configuration as per steps described above and was able to connect to the board from FreeMASTER GUI.
Note: by default SDK enables CAN abort mechanism, so I had to disable it manually:
/* Enter Freeze mode */
CAN0->MCR |= (CAN_MCR_FRZ_MASK | CAN_MCR_HALT_MASK);
CAN0->MCR &= ~CAN_MCR_MDIS_MASK;
while((CAN0->MCR & CAN_MCR_FRZACK_MASK ) == 0){}
/* Disable abort mechanism MCR[AEN] = 0 */
CAN0->MCR &= ~CAN_MCR_AEN_MASK;
/* Enable the FlexCAN module */
CAN0->MCR &= ~(CAN_MCR_FRZ_MASK | CAN_MCR_HALT_MASK);
Hope it helps,
Iulian