I have been dating my boyfriend for two years now, we have never used any other protection other than birth control, and I now have the para guard. He recently started developing warts on his shaft. I am confident he has not cheated on me, I believe he got them for his ex, before we met and they were dormit. He went to the doctor and they diagnosed him with genital warts, I have been tested as well and my paps have come back negative. I have also had the gardasil shot ( all three ) close to 6 years before him and I met. We have not had sexual contact since he was diagnosed and he is treating them currently, my question is despite the fact that my results were clear of hpv is it possible they may occur later on ? How will warts affect our relationship? Can you have a happy healthy sex life with warts? I don't want the warts, but I do not want to break up either. We have a very happy relationship, and I can't see myself with anybody else.

Any advice will be appreciated.

Yes, it is quite possible that they were dormant in him for quite a while, which is one reason why they can get passed back and forth between sex partners. They are harder to treat in men. If you get them, you can still have a sex life with him without discomfort, generally, but I wouldn't, until he gets a clean bill of health.
You can spend hours googling and reading about this subject, and I would suggest that you do so.