Following a number of issues I've had with YouTube responses, I've been doing some research. I found a possible reason why videos are losing their response. Apparently you can only add your video as a response to one video. This means if you add it to more than one you will lose the previous link. But this also can solve the problem for missing videos responses. As your video can only be a response to one video what you need to do is you need to "Post the same video as a response to one of your own videos, and then refuse to accept it. That will cancel the current one." Then you can add as a response again.