If you used the FNV 4GB Patcher to enable the use of more than 2GB of RAM, you will need to re-run it after re-installing files. Now you can restore your backed up "save game" files to the "C:\Users\<YourAccountName>\Documents\My Games\FalloutNV" folder. However, before loading ...
Assuming you have patched your game with the FNV 4GB Patcher, you should now be able to run "FalloutNV.exe" and have NVSE functional. If you haven't patched, then run the "nvse_loader.exe" file per it's instructions instead of the "FalloutNV.exe" to launch the game. Either way, ...