After you get the armor upgrade on ED-E everything in his inventory was gone(not sure if its supposed to happen or not). About 15 minutes later I stored brotherhood power armor on ED-E and I look at his inventory again and the armor dissapeared along with some other random clothes. anybody else have this problem?

I heard of this. I'm pretty sure it is meant for his inventory to be wiped after getting upgraded. I read this when the game was first released to take everything out of his inventory that you want

Yep... I guess it can kind of be considered a glitch, but from a programming standpoint the ED-E you get back isn't the same ED-E you gave them (for some reason instead of just re-skinning him, the game removes the old ED-E and replaces him with a new one, so there's technically two of them).

Also, you can't give ED-E any faction armor (you can't give any companions faction armor with the exceptions of Boone who can wear/hold NCR armor and Veronica who can wear/hold Brotherhood armor), so if you gave him Brotherhood Armor after the upgrade and remember where you did that, the armor is likely laying on the ground/floor somewhere in that area. They just automatically reject/drop armor they're not allowed to use.