If you have good batteries in all your remotes and any keyless entry and they all worked together previously then you likely have a failing remote. It is not uncommon for one failed remote to cause problems with the others ability to work. Sort of a case of one bad apple spoiling the whole bunch. What you need to do is find that one bad apple, in this case it is the one that works but causes the others not to work. It is helpful to mark the remotes somehow as 1 and 2 or something similar.
Double-check all the remote batteries are good, and then erase the memory on the overhead unit. Program any keyless entry first and check that it works. Once the keyless is working, program remote 1 and then test it to be sure it works the door. Now try your keyless again, does the keyless still open the door or did remote 1 wipe out its code? If the keyless entry no longer works then remote 1 is bad.If everything still works then try the process over again with remote 2- wipe memory, program keyless, test keyless, program remote 2, test remote 2, check if the keyless still works. If not, remote 2 is bad.The process takes some time and it is easy to confuse yourself, which is why it is good to mark the remotes. But the end result is usually the need to purchase one remote for a small fee rather than having to purchase some larger component, such as a logic board, that could cost almost as much as an entirely new opener. Just be sure you purchase the correct replacement remote for your model or you may end up having to go through the whole testing process again.