If the item is a base item (not part of any mod), then it should still be present after you disable other mods.  Make sure to backup your character(s) and shared stash first, or otherwise you'll probably lose items.

My mods also add some attributes to the game that items have a chance to get ('attributes' as in "+3% attack speed" or something), so taking off all of my mods will delete everything. I only know this because it's happened before, ha.
Like I said, the bug isn't a huge problem, and seems to be very specific. I don't personally think it's worth all the trouble trying to figure out why it's happening.
Speaking of bugs, though. I was actually playing a little today and it seemed to me like some of the skills didn't work like they're supposed to.
Flame Bolas doesn't seem to break shields? (Not sure if it immobilizes.)
Command isn't always active; it's only active for the duration of most of the cooldown (about 28 sec out of the 30 sec cooldown). I'm not sure if that's intended. From my understanding, it's supposed to be a 'toggle' kind of buff, since the icon stays on your screen once you activate it the first time (although it only shows on your pet and other people you're playing with). It's hard to tell from the description exactly how it's supposed to work, though.
I would ask other Vanq players or test it on your own game to see if it's because of my own mods or not.. heh.
I don't really see how, though, as this mod is above any other mod that would affect that. But I also don't know much about modding, so.