From my experience, you should still be able to connect to the board and program it, even if the pin configurations get changed/messed up. You won't be able to read/debug the device, but I would expect you to be able to just program the board with your new code using the SWD jlink.
Your response is the same as description in the project (when using GPIO debug instead of SWD). But when I use Jlink to connect to the board, I got error: Could not establish a connection to target. so I cant up my new code. Do you have any idea? Thank you.
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Try plugging in the jlink, then power-cycling the board; The miniprog3 (if that is the one you are using) allows you to power the board through the programmer, so plugging in the jlink, then powering the board through the jlink connection might yield results?
Otherwise, if you can have the jlink connected while powering on the board you might be able to re-establish connection.
Thank you so much, it works