Question about FLEx file placement

[Vehicle]

I seem to have run into a snag with FLEx (surprising, right?). Im using the program for the only thing its good for - creating bases (bare bones i.e. no commodities, missions or anything, just the model) however, I can’t seem to find the system folder anywhere. I’ve tried dragging and dropping from FLEx onto the desktop but it says its no longer there. The mod folder that features this system is empty save for the script. Despite this, FLEx will allow me to edit and add bases to the system. Can someone help me understand whats going on here and how, if I can, fix it?

For those who need visuals to gain a better understanding:
http://i.imgur.com/Qyx5S.jpg - Shows what FLEx sees in the mod folder versus what is actually there (which is nothing)

http://i.imgur.com/o0G7G.jpg - Shows the “lolitsnottheredude” error.

Thanks in advance.