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I don't think this is possible as the checksum on the ROM will be different which causes a reset. The best you can do really is write down the scores before changing it, at least you'll know if you've beaten them yourself then.
FYI I just applied the non-ghosting patch to The Shadow ROM version LX-5 and it retained all high scores and audits (to much relief!) even though the checksum was different. YMMV
I wasn't expecting the high scores/audits to be saved either (I made a note of the important ones before the swap - didn't want to lose my 15 year high score!). I wonder if there is something in the patch that tricks the game into thinking its the same ROM even though the checksums were different.
LX-5 Checksum: x02D1A205
MX-5 Checksum: x02D1A505
BTW the patched worked successfully. There wasn't much ghosting before (really had to look for it) but now it's been eliminated completely.
When I converted all my games to NVRAM I had the same idea how nice it would be to keep my highscores on all my games (I´m a bad player and it would take me forever to reach them again)
So I came up with a procedure how to recreate/write your highscores (or even some fake ones to impress your mates if desired ) into the the NVRam chip.
Described the procedure here: https://pinside.com/pinball/forum/topic/restoring-writing-own-highscores-to-nvram#post-6623549
prerequisite: One needs a (Eprom)programmer and the CPU converted to NVRAM
Dont think it matters what the eprom name is - whenever I alter any roms you have to get the checksum the same as what it was before. The only games I have done this with was Theatre of Magic and another WPC security cpu era. You can have fun with the WINNERS DONT USE DRUGS frames......
If you are really worried about the high scores - note them down.
Then play a game with the 'glass off' and get a score close to your previous games.
Very curious to see if you do keep your scores etc.