The odds are always better that a new positive test result or newly emerged warts are from a recent encounter than a past one from years ago.
BTW, the term clearance does not mean your body removed the virus. The medical community thinks that the virus never leaves the body. It just means you may not be infectious again.
Unfortunately HPV can be carried for years before it emerges. Meaning that a person could have a partner, break up, get a new partner, be with that new partner for years and give them HPV (from the last partner) and it might not appear until years later. It makes a lot of people think their partner isn't being true to them in this way. In regards to clearance, there is some literature out there that indicates also that numerous strains of HPV (there are around 100 now) can clear the body on their own by 2 years (faster if one takes on a healthy life style).