question about sprite backup and restoring after flashing custom rom...

[ou2mame]

i've never tried to restore after flashing a rom. say that i try out a rom and don't like it, and i reflash the stock rom and restore a backup i made, will all the files that i've changed restore as well? specifically, files such as manilla mods, and things that i've added to the windows dir that resco warned about being rom files before it overwrote them.