Do you have pics or a link to this VE-1 you're talking about?
As per your questions and concerns, obviously with the released of the VE-1 and VT-1 version 2 has affected the value of the vintage 1/55 VE-1. Not only that, but a flood of Macross goodies which are far superior than the 1/55 in terms of articulations, anime line art, accessories, tampo, countless features, price, etc...
Even if you want it to be AFAed, I don't think you'll get your money back at all. Unless its for personal collection where you want to put it up like a shrine, sure. Personally, for MISB VE-1 I would probably willing to pay about $600-700 bucks. But that's just me.