Yep, most mods make some nice changes, but unfort FLMM isn't 100% reliable. Sometimes it will delete or not restore old files back to their rightful place. Heck - sometimes it just doesn't uninstall the mod full stop. You can use the SDK to "replace" some of the files - basically the data folder ones, but it won't replace the Freelancer.ini file, the dll files (if the mod replaced one) or the mpnewplayer.fl and newplayer.fl files. Personally - back up your EXE folder and donwload the SDK.
At any time you can then install the SDK and restore your EXE folder back. Best thing is that it won't take much space/time - whereas as good as the other suggestion, it will take about 600Mb of space (this way takes about 20Meg or so)