Tell me about it, I lost most of my mods and can only be used as AI aircraft. Really miss my Star Wars mods. Big deal when mainly playing single player and creating missions around them.
There seems to be an update that includes FC3 modules and security against piracy. It causes user mods that use FC3 such as the Su35, star wars mods, F-35 etc not to be able to be put under human control and will only work in AI mode.