I sent my ship (Albatross) to a science fair, there I got a chemfuel reactor, when going back the ship landed and disappeared with my passengers leaving nothing behind, I loaded my save before launch and sent smaller ship, this time the ship came back and only shp disappeard leaving only passenger (ship disappeared along with items) so i checked something, the ships have a problem with mod to minify machines, when they fly back they try to unload their items at the place, in case of that mod they try to place the machines back at the place instead of their minified versions so they take place of ship/passengers/items that could be unloaded at the place so the whole ship/passengers disappear while trying to place those machines, which in the case do not get placed after all cause theres no ship to place them from so whole thing disappears along with its cargo. I hope that helps a bit in understanding the problem.