I'll admit that I don't know anything specific about your piece or how the window operates. However I worked as a supplier to honda (as a quality engineer) and have some experience with honda product testing. As a general rule, honda wants to eliminate anything that isn't necessary.
I would go to your dealer to get it fixed, because this could easily be your chance to prevent your window from getting stuck, not sealing well in the rain, getting scratched etc.
My quess is that they are window guides and got knocked off while some hack was trying to learn how to use a slim jim.

my $.02

 

lol dammit i'm definately not letting the dealer near me do this...they are freakin retards. and do you know how hard it is to contorsion twist your arm to the place i think these things belong??? and then not being able to actually SEE where i'm putting them...sigh this is gonna suck...seriously though where on the upper door do they go? towards the mirror? towards the back of the car? i'm guessing they're a guide for the side of the window pain as its going up and down from what slows2k put. and i highly doubt it was someone slim jimming the car for the simple fact that the drivers side one fell out during normal window operation and the passenger one was prob in there for a while...i would think if the nubcake couldn't get the one side he would just stop for the simple fact that the other side is the same pain in the ass as the first was...that and it doesn't look like any nubcake slim jim damage to my car

 

They may be old ones that got knocked off during a regulator replacement. The clip inot the to of the door frame between the glass and the door. Buy a service manual and you can get a pretty good idea where they go www.helminc.com