you play mugen using bat or cmd file and make a loop check to mugen.log and give timeout like 5 second or what you desire to save cpu. which mean during you play mugen the batch will always check mugen.log every 5 second to see if the string found at mugen.log (when ending credit after arcade loaded (that should be the string)).if the string exist in mugen.log then rename a secret character folder in chars folder to match with what listed in the select def using a batch script. also make a check for second string if ending credit end string found in mugen.log, you restart your mugen thru batch script and able to see the unlockable character instantly.
theres a lot alternative method actually
you need to study how to loop in batch file