With the recent rash of vehicle break ins, where the garage door opener and registrations were taken – first thing you need to do is make that old opener not work. First – unplug the opener. That is quick and dirty but will stop them until you take a more permanent step. you need to make that old opener useless permanently.
Some older models there is a set of switches on the opener that set the code. The remotes have the same inside. Just flip a few of the switches on the opener to the other position and then make the switches in any remaining or new remotes match – job done.
most newer openers learn the remote and will have a button to make it forget the remotes (all of them). Then you need to have it re learn the existing remotes or the button built into newer vehicles. Then the missing remote will be useless ( unless it is recovered and then you can have the opener re learn it).
There may be a different process for the openers that are IOT (Internet of Things) connected through wifi.
DO NOT, as someone posted in a comment elsewhere, booby trap your car to injure the thieves – in today’s lawsuit happy world – not a good idea! Besides it would probably damage your car and the insurance might well decline to pay.