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The bootloader for this product is fixed to 9600 baud rate for 4MHz crystal.
If the crystal frequency is increased to 12MHz, we assume that the UART baud rate should be 28800. You need to take care to increase the baud rate of the Flash programming tool. As I know, the Cypress tool is not supporting 12MHz.
Alternatively a synchronous UART communication can also be done. Find more information in the MB91460 TRM.
Here an abstract of this chapter:
Be also sure that boot security is not activated, otherwise, the internal bootloader is skipped.