"(a) What is involved in time and money to get a new set of deeds, is this even possible - reading some of the previous threads I was not sure it was."
Yes, its possible - very much depends on the type of title. If the vendors solicitor has been in touch with your own solicitor, they'll have discussed the various issues so your solicitor should be able to give you time frame/ cost implications advice.
(b) The indemnity policy that is being offered - will we have to pay anything on that in the future to keep it active or is it the responsiblity of the bank to always honour it?
Again, it depends on what is on offer.
(c) Would anybody consider this problem to be a deal breaker or is it fixable once the correct documentation / cover is provided by the vendor and the bank?
If its fixable ( not all of them are) then it should not be a deal breaker
mf