If your ED-E was still storing items when you had him upgraded, all your items will be "lost" when you get the ED-E back.
To fix:
Open console by pressing ~
Type prid 1732cf
(if that ID doesn't work, try 1732d1 and 1732d0)
Type OpenTeammateContainer 1
The old ED-E's inventory will open and you will be able to take all items from it.
To fix:
Open console by pressing ~
Type prid 1732cf
(if that ID doesn't work, try 1732d1 and 1732d0)
Type OpenTeammateContainer 1
The old ED-E's inventory will open and you will be able to take all items from it.