I suppose you launched FL from the FLMM and the Load-window was empty. Reason: FLMM loads save-games in a different manner than FL without FLMM. FL-Save-Games are on C:\My Games\Microsoft\Freelancer\Accounts (or somthing very similar to that).
FLMM saves the save-games in the same directory as flmm itself (normally: C:\programs\flmm\accounts).
So just copy your save-games from one into the other account and you can run even an unmodded game from FLMM.
Of course in most cases you cannot transfer save-games from one mod to the other (game crashes most probably). So if you begin to play a mod you normally have to start a new game.

Thanks

The art of flying is to throw yourself at the ground and miss.