When code in KSK-MB9BF506R internal flash sets the pins needed for JTAG/SWD in General Purpose IO mode, JTAG/SWD access will stop working.
On MB9BF506R, the pins used for JTAG/SWD can also be used for General Purpose IO.
When these pins are used for IO, it is not possible to access the MCU via JTAG/SWD.
It is possible to program internal flash such that only way to restore JTAG/SWD access is to erase the internal flash via other means, for example using USB or the UART.
For USB, you can connect JP4 pins to each other, (i.e., MD0 to +3.3V to get Serial Write) and P22/SOT0_0 via a 10k resistor GND (to select 4MHz).
The UART (P21/SIN0_0, P22/SOT0_0) is not wired to any appropriate connector in KSK-MB9BF506R (as of August 2011).
Thus H/W modification is needed to recover JTAG/SWD functionality in these cases.
Please see board documentation and MB9BF500 series flash programming manual for more details.
See also the Software updates for starter kits page, where you can download the schematic for the board.
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