vandy just about covered it all, but I would add that if the strain of HPV that you had years ago is the same strain that your current boyfriend has, you can not catch it again. HPV is like every virus, once you catch it one time, you can not catch the same one, your body builds immunity to it.
That said, there are several strains that cause warts, so it is possible that you dealt with a different strain than the one with which your boyfriend is currently dealing.
Well, obviously your original case of warts is long gone. His I'm a bit confused on. Did he say he got HPV from his wife three years ago and then 9 months ago he had sex with a woman with HPV history? If so, then the case he got from his wife I'm assuming was warts as if it was high-risk HPV he'd never know for sure as he'd have no symptoms. I'd wager that the infection from his wife is gone now, too, which would mean he has it from this protected episode. That's not a golden rule, just a surmise based on the HPV knowledge base these days. In that case, his HPV may not have reappeared at all, rather, having a new case of HPV appear for the first time.
Remember that when we have protected sex there is often foreplay that is not so protected. Things can touch down there before a condom is donned as well as the base of the penis is still exposed and so it's common enough to get HPV still that some people claim condoms are only 70% effective against HPV.
I can understand your terror about contracting HPV again. After the warts are removed, you can feasibly begin having protected sex again as soon as he's able to handle it. My ex and I had loads of unprotected sex while I had HPV and she never got it as far as we know. Neither have either of her two subsequent partners. I even had an outbreak while with her (it was a long distance relationship) where I had an outbreak about five days after we had sex, and then we resumed having unprotected sex again about a week to ten days after I had them removed.
As far as the chances that you will contract his strand of HPV, I do not know about that. I'd say it ranges in the area of likely to moderately likely but I have no way of knowing whether that's true or not. My buddy is dating a woman now for about nine months who has an active HPV wart infection. He doesn't have it and they don't use protection. My advice would be to remember that warts are just a cosmetic issue only and will go away in a couple of years max so just live and and do your best to avoid but if you can't then just go to the doctor and have them removed. HOpe this helps.