Nevermind, found a fix. If you place some model files in your game's Design directory - then you couldn't save it properly even as another model with another name. Your edited model will show only original parts, even in edited places, scale, rotations, but all other added will not be shown on model and will be shown in parts list of model. If you previously move your model files in to My Games\GalCiv3\Design subfolder as all other Steam Workshop models go, then you could edit your models whatever you need and save them properly.