Sounds dodgy to me the amount of work involved in modifying trusses to complete loft conversions is usually not worth it, I have done a couple of truss roof conversions and luckily both have been detached properties and we have stripped and re-cut the roofs, modifying trusses is a complicated job involving usually several steel beams and timber structural stud walls. I would be very surprised if this has been done properly in your case, as the surveyor has picked this up, but check with the owners and local building control because there is the possibility that it may have been done correctly. Your solicitor should have been asking these questions with regards to modifications done to the property.
If you are serious about buying this house then I would speak with a SE and find out what needs to be done and then get a quote for doing the works and adjust your offer accordingly.
Remember that if you don't carry out the works within the period specified by the mortgage company not only will they retain the £5000 but they may also withdraw your mortgage offer and demand a full repayment, also when you come to sell in the future you will quite likely run into similar problems yourself.
Get them to reduce the price or walk away, would be my advice, there are times to negotiate and times to walk away.
A couple of years ago I spent nearly £3000 on the preliminaries to a house purchase, including paying the owners mortgage for 2 months, my solicitor found an irregularity over the ownership of a piece of land that we would have to cross to access our property, apparently this had been messed up by the land registry 2 sales ago. After investigation my solictitor advised me to walk away as it could take years to resolve and that the neigbours would be legaly allowed to fence off the piece of land and deny us access across it if they so desired.
Anyway we walked away and two years later the matter still hasn't been resolved the property remains un-sold and there is a notice on the land registry which states that the property is subject to a land registry investigation, so no-one will go anywhere near it.