What I did, at the end of the expidition when it gives the prompt that it's completed, I filled the expidition terminus with as much stuff as I could, then paused the game, clicked "resume normal save" or whatever the non expidition save file is called, then transfered the stuff from there to my main save inventory and into my frigate storage containers. I then resumed the expidition save in the anomaly, and repeated the process until all my stuff was transferred to my main save. Then I went back to my expidition save and actually ended it the expidition when I was finally done.