If you bought Mushihimesama or Espgaluda II Cave SH3 boards used, chances are you have a bunch of very high scores logged in the permanent hishscore section, with no chance of entering your own initials - outside of "Today's Highscores", which erases when you power down the board. So what's a mediocre shmup player to do? Well thanks to kernow for starting this thread on the shmups forum, and to rtw and idc for replying with an answer, I bravely tried the procedure on my Mushihimesama PCB.
**** WARNING! **** I take no responsibility if these instructions lead you to frying your PCB. Proceed at your own risk!
What you need is a 100 ohm resistor (pictured below is actually a 97 ohm precision resistor).
With the PCB turned OFF, first remove the battery, then put one end of the resistor to ground. You can use any ground. I found the hole of pin 5 on the missing serial connector a good place so it wouldn't move. Then carefully hold the other side of the resistor to pin 9 (Data Output) of the RTC/EEPROM (U10), and power on the PCB. The bootup sequence will first check the program code, and then checksum the EEPROM. Its at this point, the checksum will fail, and the board will re-initialize the EEPROM, so quickly remove the resistor as soon as you see the EEPROM "initializing".
Since these surface mount chips are very small, and you don't want to accidentally ground other pins on the RTC chip, I used an exacto knife to cut and place small squares of electrical tape to isolate pin 9.
You can verify the procedure worked by going into the operator menu and checking the ranking display. Here is the before and after shots of Original mode scores on my PCB.
Note: Ibara, Pink Sweets, and Muchi Muchi Pork have an operator menu setting to clear the ranking display (thank you Mr. Yagawa!). Deathsmiles also has a reset ranking option. I do not know if Mushihimesama Futari or DoDonPachi DaiFukkatsu boards have this option as I do not own these yet. :)