Dunno if any of the Cave-STG regulars saw this in the Shmups forums, but it is of very relevant interest to me since I need to erase the damn high score table for the Mushihimesama that I bought.
http://shmups.system11.org/viewtopic.php?f=6&t=39330Remove battery. Short pin 9 (DO) to pin 12 or 13 (GND) and power on. Wait until EEPROM test, watch for the word "INITIALIZE" and remove the resistor.
This works, and the game will re-initialise the EEPROM.
Pictures courtesy of rtw


Or...

Cover up the other pins on the chips with electrical tape to make sure you won't do anything funky. You can use a regular piece of wire (kernow method) or a 100 ohms resistor (Dave K. method) and either way it will work just fine.
Note that this will relock Ultra mode on a game like Mushihimesama (non-fixed) due to the reset of the whole board. But that way you can build up a real Maniac score list before it ruins the Ultra score list.