You should be able to swap out batteries fine without having to reprogram. I've never done it to my factory remote, only use it when I don't want to set my alarm, but I've changed out my alarm remote battery twice now. Just pop it open and change the battery.
"I'm not driving too fast...just flying too low"
-03 SB Cobra vert- 2552 of 5082 Born 02/25/03
90 7up vert - new project-07 DSG Focus -DD