Yes, for most people they don't come back after 6-24 months. What triggers a relapse is unclear but it may be something that lowered your immune system. Cigarettes is usually one of those things as is alcohol. Sounds like you had multiple waves of warts from your description and you never did clear it. Yes, warts are just a cosmetic thing but if you're in a relationship with someone, then you become more infectious with warts present.
No one knows who will be in the lucky 90% that make the virus dormant in their system. No one knows who will be in the un-lucky 10%. Since men cannot be tested, we have no idea which bucket we are in. Based on theory only, the immune system is what determines this. I have given up alcohol to prevent waves as my second wave came after drinking beer. Does this mean I can't drink at all for the rest of my life? I have no idea. Do I want to risk a third wave just to get drunk again? No. I miss drinking a lot. Have no idea how I will get thru a NFL season without beer.
Maybe you should try completely quitting the cigs to see what happens?
I'm in agreement with veryworried. Another thing I might add is this. Since your experience doesn't neatly fit in with the 90% norm, I think it's time to take a closer look at what's going on. As I understand, you have no warts present right now. If you should notice any more pop up, I would definitely make it a doctor visit triggering event. Find yourself a doctor or dermatologist who will biopsy the warts and who will listen to and take your story of being in this 10% group seriously. It's almost like an episode of House. Do you really have warts still? Are you mistaking something else for warts? If not, what's the deal with the warts you are getting? A biopsy will tell you for sure and that's why I'd insist on having it done. Do not let them simply freeze it off.
Have you heard of Podophyllin? http://www.webmd.com/sexual-conditions/hpv-genital-warts/podophyllin-resin-or-podofilox-for-genital-warts-human-papillomavirus In my case, I'd had five outbreaks in a year. My fifth visit to cryo the derm applied it. I came back a month later for another application. I never had warts again. Did the pedophyllin do it? I don't know. But the concept is cool. If warts are lying around in your skin cells waiting to erupt into warts, then fukking them up with skin cell damaging resin sounds preventative or even better. Give it some thought.
It's possible you have a strain of HPV that is ornery and persistent and just doesn't like to go away. It might not be your immune system at all. A biopsy will help determine this. Still, why are you even smoking in today's day and age. Quit that shite right now and reap the benefits of boosted immunal health. I'm on the fence about how much we can really affect our immune systems, but then again, my immune system has always been crazy good. Still, I had five outbreaks. It was all over and done in one year though so I'm a text book HPV case. Good luck figuring this all out.