Fortunately, energy credits and gear aren't all that hard to get right now... when they start putting in really rare items they are going to be in serious trouble (god forbid I lose a purp item this way!).
Just had an item bug out on me too. Had some MKII item before but it then changed to the old weapon I had in that slot, leaving me with 2x the older gun. Very odd, thought I was going nuts but it looks like there are def some bugs with items.
This happened to me tonight as well, and once in the Open Beta. 2 Newly looted ship weapons disappeared after zoning over to do some PvP. this was after about 20 minutes and about 5 map changes. I only lost them after going into the PvP though, which is weird. It "should" have reverted to the old stuff on the 1st map change.
This is a very important bug that needs to be FIXED very soon. I reported it in game, but they were nice white weapons. If they were Rares, I'd have been very ****ed.