There's a bug which will cause mysterious disappearing weapons. It occurs on items that have been wielded at some point using the Telekinetic Grasp talent. Such items, when you try to take them off, will disappear forever. Worse, if you indirectly take the item off by wielding something to replace it, both items will disappear.

Doh!

Now the good news:

1) It only occurs on characters that have been saved and reloaded. If you do everything in one sitting, you should be fine.

2) Yufra was kind enough to whip up a very quick fix and post it here: http://forums.te4.org/viewtopic.php?f=42&t=24592

Sorry for the inconvenience!