2000 Keyless remote question

I recently had my 2000 in the shop for an alignment. Much to my horror, when I picked it back up the remote for the unlock and power doors was missing. Shop owner swears it was on the ring when he parked it outside.
Anyway my question is this: I am getting a new key fob, and have the 2nd stock one with me. When I go to program the replacement the manual says I need to hit the button on all remotes to key them the same. If I do this and the one that is lost shows back up in the hands of someone else, will that remote still work on my van? Or will it not work beings I redid the code and only pushed buttons on the two remotes in my possession?

If you reprogram any remote yourself, it will erase any prior programming. In other words, the "lost" remote will not work if you reprogram your remote that you have. I hope this helps.

Exactly. Once you enter programming mode, you delete the previous stored memory.

Any remotes you have now, including the currently programmed one will need to be programmed together.

that's what I was hoping for, thanks for the quick response to ease my mind!!