Hi,
What you do depends on your mortage company - they may withhold the £3000 back form the mortgage for the work in which case you either have to negotiate with the vendor to get them to reduce the price by the whole amount or if you do have some spare cash explain the position to the vendor and state how much you can afford towards it and try and get them to meet you on this...
Just be upfront and honest - if ou have a good relationship they should respect the position you are in - after al lthe valuation was made on the basis of no work being required and they should appreciate this.
Good luck