I think that, even though your automatic saves (the "before port" and "leaving port") will be overwritten with your new career, you can still use your "on mission"-saves that you save yourself, if you know what I mean...
IŽd say, go on a mission with your old career, then when just leaving port, save your game with a special name for that save. Then start your new career.
A bit messy but I hope you get my point.
Good luck!
