2002 Toyota Sienna Door lock/keyless entry

I was in a fender bender, on my passenger side. I had the fender and passenger door replaced. A few days after pick -up my remotless entry stoped working. Then I blew a fuse to my dome and clock. I replaced the fuse and everything worked again, including the keyless entry. Then a week later it stoped and when ever the passenger door was opened and shut a clicking noise followed. Like the locks are opening and closing. I took it back to the shop and they say they replaced the actuator but are unable to program the keyless entry. They say it is the failer of the keyless entry computer and that it is not related to the accident. The passenger door still makes the clicking noise when ever it is opened and closed. So, I see no change from before the second repair. I was wondering if the repair shop has damged something when fixing my door or is it a coincidence that the passenger door clicks and the keyless entry no longer works.