When you program one remote and the other will not work, there could be a couple different issues.
If the remote is not compatible to the opener it will not program. Click on the chart below to check the compatibility.
The learn button on your opener has two functions, one is to program the remotes and the other is to clear the memory of the opener. If you press and hold the learn button down even for a few seconds, it will erase any remotes you previously programmed. It is very important that when you press the learn button, that it's a quick press and release.
Quickly press and release the learn button.
Press and hold down the button on the remote that you want to program.
Hold the button until the lights on the opener flash or you hear two clicks.
To program the second remote follow the same steps.
A billion code remote and a Security+ remote will both program to an opener with a red learn button, but they will not program together. You can either have billion code remotes or Security+ remotes, programmed to the opener.
If a you are trying to program a universal remote (KLIK1U) to the opener with a red learn button and it will not program per the instructions, check the other remotes that are already programmed. Your other remote maybe a billion code remote (green learn button), which would require you to follow the steps for programming the universal remote to a green learn button.
If you have two Security+ remotes and only one or the other will program to the opener, one of the remotes has reverted back to billion code technology. To figure out which one has, you will either need another remote or a keyless entry.
Clear the memory on the opener. Press and hold the learn button for 6 seconds.
Program the keyless entry. How to add, program or change a Keyless Entry PIN. (If no keyless entry is available, program a 3rd remote.)
Program one of your handheld remotes. If the first remote does not program, try the second remote. How to program a remote control.
The remote that will not program with the additional accessory is the defective remote.

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