As of yesterday, with version 1.3 this trick didn't work. As far as I know you need to actually build the trade ship from the planet in question. No way to change "home planet" on a particular ship.
I once had a planet with the starship bonus second to pirates or something at 54%. Makes for big numbers eventually.
I had a similar event in which I was not paying attention and conqured the Torian before I had committed to placing my own man capital and per the poor AI planning wound up having a manifactuing capital on a size 5 planet.... groan. Can you destroy/disband the colony with the capital and then rebuild it elsewhere?
GalCiv2 Forums
Mine is the same way. I can play for any number of hours as long as there is no autosave and I don't try to save. If I do try to save it is about a 50% chance of "out of memory" crash to desktop. What is worse the crash takes the save game spot with it. So if I save on an old save spot then that spot is gone also....