Wait, what? I'm kinda confused as to what exactly you're doing.
Either way, if you've properly linked everything in the editor, and the files are not deleted/moved/renamed while the editor is running, it should export correctly.
However, if you're opening the ships via File > Load ship from .ftl... option, then it might be quite error prone during exporting / project saving/loading (since the editor unpacks the .ftl to temporary files, which are deleted when no longer in use).
Try File > Include Mod and select the ship you wish to load, restart the editor, then load the ship in question via File > Load ship...
That said, as mentioned in previous posts on this page, there is a bug with the editor that will cause the game to crash if you try playing any ship created with the editor. It'll be fixed later today.
@Vhati
Gotta keep you busy somehow
