I've seen a lot of questions and comments about whether the old key fobs can be reprogrammed when the OEM remote start is installed.
When I had mine installed I only brought one key with me not knowing they were going to reprogram the key fob.
When I picked it up they handed me two new key fobs that had the remote start button on them. They also gave me the old one back and told me it was reprogrammed. I took their word for it and never bothered trying it.
Well since I wanted to download music to the HDD I went ahead and grabbed that old key fob. It opened the truck and started it just fine.
So, yes, they can be reprogrammed.
One note though, you cannot lock the door with the button on the door with a key in the ignition. You must use a key fob.