It's only a factory reset, so nothing too bad would happen. You'd just have to re-wipe the phone before flashing.
You can flash files that reformat all of the system directories (to change between different file systems), so that would be more along the lines of what you were wondering. I wouldn't go out of my way to test it, but pulling the battery for a second and then booting to recovery should work just fine if you accidentally tried to boot without any OS.