Well this is something very hard to search online for, but I found a forum that has a Command Start Guru and this is what he wrote to re-program the remote. For which model Command start I do not know but its a start. (no Pun intended)
Push down and release the hood switch.
The parklights should come on.
While the lights are on push and release the hood switch again.
The parklights should remain on.
Push Button I on the transmitter until the lights go out.
Close the hood and try your remote .
Does that sound about right? I dunno........I'll keep diggin and post what I find.
EDIT:How many button remote do you have and whats the model number if you have it?