I've done a few mods to my mill. After once running the wrong program (I didn't watch closely enough and neglected to delete one program before loading another), I altered the BP firmware to only hold one part program. Any new program you load automatically overwrites the existing program. I also added a feature that allows me to toggle between 0.0005 increments with the hand wheel and 0.0001 increments. That is particularily usefull when hand feeding with micro endmills (the 0.0005 steps tend to break the small endmills) and when tramming a part. I redefined the illuminated MDI button, which I never use anyway, to serve this purpose.
The BP OS does a crc check when it boots (if you've had a rom failure, then you would have seen an error message saying something about crc) and I alter the crc word so that the check is still successful. If my new roms become corrupted, the mill will not boot.
Yup, I have too much time on my hands. And it's kinda fun digging around in someone else's programming.