Help Problem with Locking & Anti-Theft

Hey guys well let me tell you my story. I have an '06 mustang which was involved in an accident...some girl smashed into my right side as i was passing her on the side and totally destroyed the right side fender and scratched the car all the way to the back...

My Doors were locking perfectly before and after the accident with the remote. One press would lock and two presses would beep the horn and flash the lights real quick. Here is where the thing gets messed up. I dropped off my car at a body shop to get repaired and after about a week I got the car back looking perfect.

I get home, park the car and when I am about to leave the car I hit the remote twice to lock the doors and hear the beep like I am used to hearing... Instead I get this: the doors lock and I get 2 beeps and my lights don't flash... wtf? I am not sure if the locking anti theft is working correctly anymore? would disconnecting the battery for a long period of time mess that up? would it need reprogramming? I am just concerned because I get no indication the doors are actually locked...I have to physically check them both now everytime its driving me crazy... I hope someone can chime in please. Thx

this is a late response but u were absolutely right 09v6! turns out it wasnt the doors at all. the problem was in the hood. when they removed the fender, they had to remove the hood switch and they never put it back on! so the alarm kept thinking that something was open. Its all good now lol. just thought I'd share this in case it happens to someone else you know.