When the new GMS contract was introduced in 2004, practices became responsible for paying employer's NHS superannuation for GP principals. Previously the PCT paid this directly to the NHS pensions.
From April 2004, practices' funding was uplifted to include an amount equal to the cost of the employer's contribution prior to the new contract. GMS practices' global sum equivalent and PMS practices' baseline funding was increased for this.
If a partner in a GMS practice chooses to take 24-hour retirement, there should be no change to its funding, so I do not agree with the PCT's action. PMS contracts are locally negotiated and PCTs' treatment of PMS practices does seem to vary. However they should not be disadvantaging your practice compared with GMS practices. I suggest you raise this issue with your LMC.