It depends. You can erase the memory of the receiver by locating the smart/learn button on the motor unit near where all those white wires go. Press and hold this button for 6 seconds and then release. Neither of your remotes should work at this time and neither will the missing remote. Now you need to program the remotes by pressing and holding the button on the remote while you press and immediately release the smart/learn button. Do this for each of them. Here is where the catch comes in. If your missing remote had exactly the same code as one of the two remaining it will also open your door now. The only way to eliminate any possibility is to buy all new remotes erase the memory as above, program the new remotes and never again use one of the old ones.

Don,
I also have a programming issue with my 139.53677SRT1 and have read many of your posts. Great help by the way.
Just tried your programming steps (Hold the button on the remote and then push quickly the LEARN button) but the LED on the GDO lit steady for 5 seconds then went off and the programming did not happen. Any other idea?.
Thanks a lot for all your posts.

charlie I answered your post above. I'm now perplexed. It now sounds like the logic board. I hope you have a friend or neighbor you can experiment with.

Kitkat,

You need to just push the learn button down and release & the amber led will lite next to the button. You then get about 30 secs to push the desired button on the hand remote. The light will flash twice when programmed. It's programmed. Do the same the other remotes to program them.