That is a glitch I noticed myself too, if you give items they can not equip they should return to your inventory or stay in theirs. I hope it gets fixed very soon, because a lot of my loot is Apparel.
Reno
I at first believed this to be a glitch too (still may be) However what happens when you see the pop up that your follower can't use this faction's armor means they drop it on the ground. They don't keep it in their inventory unequipped. At the repconn hq I had this happen where the armor fell underneath the fallen ceiling so it was unrecoverable. Thankfully was able to load right before that event. This is true of any follower not just E-DE.
However, I have lost E-DE somewhere during the Volare SideQuest and can't find it now. Veronica had I suspect a similar issue with the end of her Side Quest. I was wary even before completing that quest as she wouldn't zone into the building. After the event I noticed she wouldn't leave with me either. Ultimately I stripper her inventory and told her to hit the road before she started walking back to good ole 188.