Similar situation happened to me yesterday.  I started an emerald void crusade with my lvl 84 Crusader and all my gear was gone on the first mission.  Everything.  I abandoned the crusade, went back the main bridge and still everything gone: my equipped gear, gear in storage and I noticed that all my previously known blueprints are gone.  I've tried contacting Neocore through chat but that's not getting anywhere.  WTF?