Currently I have a  Colt MT6400C and Armalite M15A2 20" (both preban). I am deciding to either leave them stock and buy an new m4 version with all the evil features or modify both of my current rifles. If  I end up modifying, I would put a collapsable stock and flash hider on the Colt and bayo lug and flash hider on the Armalite. Would these modifications hurt the value since they are both unfired and NIB or would they help the value. Any input would be great.

Sorry, I am an idiot! The rifles are post ban "no evil features"

Did you get your rifles for an investment or to shoot? If as an investment I have some advice for you. Please go and shoot them. Rifles were built to be shot not looked at.

I acutually shoot most of my guns but have not had time to shoot these two as of yet. I just dont want to start changing things on two brand new guns that will hurt its value in case I ever have to sell them( God forbid). Kind of like buying a brand new Infiniti at the dealership and driving it straight to the body shop to put a new coat of paint on it. This would obviously bring down the value of any car with a second paint job (unless it is a collectable). I am just wondering should I buy a new one with all the good stuff on it and keep my other ones stock or go ahead and modify my current rifles.  

Change what you and keep the original parts.  If you shoot them at all, they are no longer NIB, so that'll be out the door.  If/when you sell them restore them back to original and sell the parts you have left, better yet, build a rifle with the parts you have.

I actually built a midlength carbine upper, just because a vendor accidently sold me a midlength gas tube instead of a rifle length tube.  I felt obligated to, what else was I going to do with a midlength tube?!?!?  That is the truth.  I did get lucky and stumble across a decent midlength barrel in my quest for parts, so that sped up the process quite a bit.

Basically, if I want the rifle to be worth more leave it alone and shoot it stock or not even at all. In order to get the Colt and Armalite "evil" there is machining to do on the barrel because of the way the manufacturers put the muzzle brakes on. Which means I can't puton the old parts back on can I? Do you think I should just get a new one?

Get a low round, used rifle and shoot the snot out of it.  Best way to go and it keeps that NIB smell on those rifles.