stamp duty to be paid twice is this right ??

A good friend (honest) of mine is selling self contained his flat (purpose built 70's? block) His ownership currently is described as a flying freehold (Though nothing overhangs, encroaches) The purchaser's mortgage have insisted that it is changed to leasehold before they lend on it. His sols tell him that stamp duty may be payable in respect of both surrender of freehold & grant of new lease @ 1% (= 2x 1320 = 2640 Total) However if Inland rev deceide transaction linked S.Duty will be @ 3% (=2 x 3690 = tot £7920)
The managment co for flats has refused to pay so if he wants the sale to proceed he has to pay all of the ammount + both sides additional sols costs.

This does not sound correct to me. Can his sol said to be acting in his best interest.(He has to sign 1 hell of a disclaimer)

The new owner will of course pay stamp duty as well.

I understand this is difficult to comment upon but some humble opinions would be most gratefully received.
hanks