When John disappeared, I altered your memories to not include him, as well as the memories of most of your friends and family. Not everyone remembers him or the fact that you two were together. As a matter of fact, Rodney didn't immediately remember about it either. But some people asked that their memories remain intact because they didn't want me mucking about in their heads.
You're not missing anything but the memories of him and what you had with him. If you want them back, I can restore them, but that's up to you. I took them because you were so tired of being heartbroken and feeling alone and it tore me to pieces to see that. So I did what I thought you deserved, I made you happy.
Because you had been so happy with John, that seeing the abject misery you were drowning in when I took him was just too much. I had no way of knowing if he'd ever be back, or if he'd even be the same John. And you didn't either. I truly thought it was something you'd have wanted but never would have asked for because you're too proud.