There are a few ways to treat genital warts... one is a topical cream. I found it didn't work at all, the doctor said it may have helped reduced the spreading of them, but there is no way to be sure. They had to be burned off so to speak. They would apply an acid to each one individually with a tooth pick. To be honest, it hurt like hell. But it worked really well. It took about 4 sessions to completely get rid of them because the clusters were all spread out and to do them all at the same time would have been very painful. This was about 2 years ago, and they never returned. I've never had an abnormal pap smear though. It's all dependant on what strain of HPV you catch. It's possibly that you re-caught a different strain of the virus. However, I'm not too sure of if it can come back unless you've been re-exposed.