If you were on AFPS75 and transferred to AFPS05 and your 'Offer To Transfer' (OTT) letter did not spell out that FTRS might affect your pension then you may have a case to challenge it with the Financial or Pensions Ombudsman:
Complaining about problems with your pension scheme | nidirect
It does say that you should challenge any Occupational Pension issues with your employer first and they must reply within 8 weeks. I know that OTT was supposed to be a one-off offer with an inability to wind it back, but did the MoD make it clear that your EDP Lump Sum would be lost if you went for FTRS in the future? It should have done as FTRS was introduced in 1997 and the OTT was in 2004/5. It is certainly worth a try in my humble opinion.
Good luck
LJ