Hi Wang,
You are quite correct. Unfortunately I can't see any way around this.
USBDM modifies the target registers to allow programming. After programming the device is reset. Unfortunately the Watchdog is not reset by a software reset - It appears to only be reset by a power-on-reset.
If you cycle power to to the target during your debugging session (and clear the USBDM connection dialogue that pops-up) you can restore the power-on-values.
Software reset in the debugger will not achieve this - The watchdog is unchanged.
I'm unsure how the Multi-link works.
bye
PS. I will modify the flash programming code so it doesn't lock the WDOG (if possible).