I would absolutely confront her about this. I would be pretty upset at finding my partner on a dating site, and if I were dating this person for a year or more, would seriously question whether I would continue the relationship. But you also need to admit you were on it too. Be honest. If you cannot be upfront and honest about everything, the relationship will suffer.
I, personally, would ask her if she is serious and if she would like the relationship to continue.
It's difficult to tell everything that happened with us. I deleted my profile in December 2015 when i became really into him. We exchanged ily in June 2016. I assumed he deleted his profile. I didn't ask anything. I trusted him. I just made a profile to see if he did chats with other women. He took the bait. Yeah it's difficult and not only is the relationship suffering but also the 2 of us.
Sorry if I can't tell everything here. i can PM.