I usually make this for my designs, as well as other embedded systems designers. I insert a debugging/service port onboard, which uses a custom protocol, and the application which uses that port is not distributed to users, it is only for service staff. So if you cannot obtain from the manufacturer the application designed to interface with that port, I am afraid your chances to do something with that port are really low. Another chance would be to extract the internal flash device and flash it with the content of an identical but working device (or with a binary file if you have it), using a programmer. This method works in most cases. Your bad luck would be a flash memory in a BGA package.....
/pisoiu