this happened to us - we were first time buyers and there was no upward chain, everything was going swimmingly until it turned out that some granny had lost her deeds.
the thing that made it seem like a genuine mistake and not a blag was that she also owned two other houses in the street and some in northampton and had lost those deeds too (and had sold no 3 a few years earlier and had had the deeds).
basically the vendor's solicitor had to 'recreate' the deeds, and this took ages. i tried ringing her on a regular basis to chivvy her along, until she told me that i wasn't allowed to do that . my own solicitor had nothing to say on the subject.
it took about 6 months for the deeds to be recreated and sent to the land registry, at which point they gave the property a possessory title, rather than an absolute title. at this point my solicitor said 'i think the land registry have been a bit pedantic about this' and 'i wouldn't touch this house with a bargepole'. but my mum rang the land registry and spoke to the woman who'd dealt with our house (i was too upset), and basically that was always going to happen - that's the law, she couldn't issue an absolute title because someone could turn up with the original deeds and claim it was their house. i was pretty pissed off that my solicitor hadn't given her 'bargepole' advice a bit sooner (before house prices had risen by over £20000 for example).
because i had already spent money and, more importantly, time on buying that house i went ahead with the purchase. this was nearly 8 years ago and no one has turned up yet claiming it's their house, not ours (touch wood), but apparently the vendors took out 'indemnity insurance' against this happening. having said that i have never seen the policy, and also have no idea whether it covers us for the price we originally paid, or what the house is now worth. oh god, i'm worried now...
i also have an idea, but i'm not sure where i got if from, that after 12 years if the original deeds have not turned up then we have kind of 'squatters' rights' and can get an absolute title that way.
the house next door that was owned by the same granny has sold twice since we bought ours and the one next door to that has a sitting tenant and has sold 3 times since we bought ours, so there are obviously plenty of people around who a possessory title wouldn't worry, but it will take a lot more time for your purchase.