So I ran the first stand alone mission 'weapons training', then landed and successfully rearmed and refueled.  I chose a different loadout from the original loadout.     
However, my weapons didn't show up in the weapons load-out page.  The new weapons did show up on the pylons outside the aircraft.  I saw a message in the mfd about 'ground safe' and hit ack twice, but that didn't change anything.  When I put the master arm switch in training mode, it showed my original loadout.  When I set it back to master arm, the pylons with the new weapons loadout were red with no text.  This was also true after I took off again (trying to see if being on the ground had anything to do with it).   
Is that normal, and I just have to restart the mission and always use the default weapons loadout?  You can't rearm/refuel in the stand alone missions?   
Thanks, 
Eagle