Hi Saiesh,
Which device is this question for?
Can you confirm if it is related to FCE2.0 or FCG1.0?
If so, yes. It is possible to flash over a different CAN channel. This can be changed through the binary file used in the CAN flasher. Please let us know which CAN channel you want to use, so we can provide you with a modified binary file.
Thanks,
Amir