If your battery goes dead and the power is turned off, you COULD lose everything including system software.
Much of what is lost will depend on which control you have. New PC controls will lose nothing except the current time/date like a PC. Older controls like the 7000 can lose it all if left off long enough.
You never said which one you have, but I'm guessing it's a 7000 series since you are getting the battery alarm about now. I replaced one on our 700L - U recently. You will need a disk to reset the battery alarm. Batteries are available online, through batteries plus or through your distributor. The disk can be obtained through your distributor. (usually for free)
Refer to this thread for some more info: