Noob questions

[Houndx]

I'm going to have two new HTC's, a pro and a mogul, soon and I'm unclear on a few things about flashing. Any help would be appreciated.

I use a regional provider, Revol, who flashes and unlocks phones with Houdini. My question is will flashing custom roms and/or new radio roms(gps enabled for the Mogul, etc) remove any of the necessary settings that were added to the phones during the Houdini flash?

Thanks in advance.