Run MGSFIX to temporarily downgrade to D2 first on your PSP, complete the first mission on Peace Walker (Not the tutorial, the first proper mission) then your safe to run MGSNEVER and go back to D3 and continue playing. Enjoy!
Or when your player dies, you can say in code, if enemy exists, do nothing, but if enemy does not exist, then create enemy at certain spot. (This would be a pain tho for lots of emeies)