It that a feature request or a question as to whether it's possible? If the latter, which is how it sounded, then the short answer of "No" is quite sufficient. You can't change ships while there is cargo in your hold. The game simply won't allow it to happen. I don't know why; maybe they fold the ships up for storage?
If it was a feature request, then that's something that actually does warrant some discussion. I'd like to see better handling of goods, myself. Once we get planetary landings, I'd love to be able to store a cache of stuff on a planet somewhere—a few rare goods as a rainy-day fund in case of disaster. Someplace to store all of those black boxes and military plans until someone offers to pay me for them or I have enough to make it worthwhile to drag them somewhere.
But as things stand right now, there appears to be no architecture in place to allow that kind of thing. I have no idea if it's possible the way the game is constructed or not. I do hope that it is.