Second vaccination? Like 12 weeks or so? It can be 14mths or so before a second testicle descends, its absolute rubbish for your vet to state that by second vaccination time both should be down.
With regard to one being retained permanently. They can cause issue in later life yes, and they do. Testicles are retained outside the body because they need to maintain a lower temperature. The body temp does alter them and can render them cancerous, of course it may be too late when you find this out.