yes. hpv stays in your system. you can have wart break outs at any time. it can be triggered when you immune system is down. if you are a woman, you may have a break out when you are pregnant. i've had vaginal warts for two years with no sign of them going away... you just never know.
keep seeing your obgyn and if you have any signs of warts, start treatments right away. your doctor will primarily say, "wait for a few months b/c your body will probably get rid of them." i did this month after month until my warts got so bad, there is no treatment. since i have them all over my vaginal walls, there is little my doctors can do. if i had gotten then treated when there were only a few, i wouldn't be like i am now.
in summary -- hpv won't go away. keep seeing your doctor for regular check ups. if you get warts, start treatment ASAP!