Its the uncertainty with this virus that makes matters very confusing. Vast majority of infections once cleared do not recur in the future, however this is not the case for everyone. While not likely for hpv to pop back up in the future it is possible but it cant be said with certainty whether its a recent infection or a recurrence of an old infection. It goes down to whether you trust your partner as she could be telling the truth.
My gut tells me to trust her - as long as there is a reasonable possibility than I will. The more I research it the more it seems like this is indeed possible - maybe not probable but at least possible. It sounds like it can take a long time for paps to not show abnormal and that most docs still don't test routinely for HPV - just as a follow up to an abnormal result.
I'm really sorry to hear you are going through this. What is your gut feeling on this?
It is remotely possible that this is an old infection she has before she met you or you infected her (from a previous romance) and it is now showing up on a test. Women have been diagnosed with it 10-20 years after infection or have had an old infection show up again 10-20 years later but the odds are not that great. The more likely scenario is that is recent (6-12 months). No one can definitely say, not even her doctor. If you love her, just move past this and know that she needs your support and that you also have what she has. It makes no sense to play detective with HPV.