If oral hpv infection is cleared from pharynx, is it safe to assume that the oral hpv infection has cleared from other proximate sites such as larynx, oesophagus, lungs, et al?

The immune system will in most cases clear the HPV from all sites at the same time to the point it is no longer contagious. However, HPV is a member of a virus family known to retain the potential to hibernate for years/decades with the potential to re-emerge. The cancer associated strains may clear initially, usually by 2 years, but trigger cancerous change years/decades later.