The employer's superannuation that is included in your PMS baseline is practice income and should be shared between the partners. As one partner is on a fixed share, the balance of profits will be split equally between you and your other partner.
Assume the two of you each have a profit share of £100,000 (which includes the income for employer's superannuation). As the fixed share partner has taken their NHS pension benefits and no longer pays superannuation, this partner can draw their full fixed share profit amount.
This will also apply to your other partner after taking their NHS pension. However, because you are still in the NHS Pension Scheme your superannuation contributions (both employee and employer's) will be deducted from your profit share and you can draw the difference.