Problems programming keyless entry..

I have just removed an aftermarket Viper alarm system.. Now I am trying to reprogram the factory keyless entry.. It seems to be not working correctly... It is a 2002 and I have read in the instructions on this site..

My question is.. When they intall these after market alarm systems do they do anything to the factory one to bypass it??

If so what do I need to do to get back to the factory system..

Good question.
You might go to the Viper web page and see what they do to install it.
And reverse it and see if things work.
Have you went threw the program procedure and then the Resynchronization procedures?
Good battery in remotes good and the newer GM/UTA remotes.
Older style will not work.
Good luck