It isn't clear if you need to permanently change the vector table or only temporarily during the bootloader activity. The S12X allows the vector table to be placed anywhere in local memory using the IVBR register. At reset this places the vector at 0xFFxx but it can be changed to any other 256 byte boundary in the local 64k memory map. This means that the reset handlers must always be at the same locations in memory but they can change the vector table location for other interrupt sources.
If a temporary change is required then you could have the reset handler choose the bootloader vector table when required.
If the change must be permanent then you will have to erase and re-program the flash block that contains the vector table. This may require careful consideration if the application requires to be functional during this process.
