I'll back you up, chief. At least in my experience with Pinbox/Nucore - completely safe, and game enhancing. Even if it wasn't, It can be reversed by reinstalling original software. As I understand it, if you attempt the upgrade with the original game Prism card and it fails you still have an out. The games original startup hard-coded software takes over:
"When you update the game, you are putting a new version of game code
and some sound data and even some image data into the Flash part on
the board. This "overlays" the equivalent section of the ROM, so it's
what gets used instead when the game boots and runs. But the ROM
version is always there as a failsafe fallback. If an update goes
bad, or the Flash somehow loses its mind on location and gets
scrambled, or whatever, the boot process will see that it is corrupt
and not use it as an overlay, instead using what was originally in the
ROMs. Thus the game will not die, will not magically be on free play,
or any other really bad problem in a location environment. And it
will still boot so you can get to the update mode and re-Flash it.
From memory (no pun intended) I believe the ROM space is 64MB, and
the Flash part overlays 4MB of that."