The answer to this query really depends on the space which the pharmacy will occupy. If the space that has been identified is currently within the space that is being reimbursed by the PCT then your reimbursement will have to be adjusted to take this into account, obviously resulting in less Notional Rent being received by the practice.
In these situations, it is sometimes possible to take the opportunity, whilst carrying out the work to convert the space to a retail unit, to try to extend the surgery premises in some way. This can ensure that additional clinical space is created elsewhere and thus the net change to any Notional Rent being received is minimal.
It should also be noted that the income generated by a pharmacy will often outweigh the Notional Rent that would have been received on the space occupied by the pharmacy anyway. Also pharmacy operators are quite often willing to pay a premium in order to occupy units in such a favourable position.
If you are considering negotiating with a pharmacy operator, it is well worth seeking advice not only with regard to Current Market Rent for pharmacy units (co-located within surgery premises) but also from a specialist accountant who can advise on the financial aspects of a transaction such as this.