Guild Wars 2

I have a Fractal Capacitor (Ascended) with Rox’s Quiver skin applied to it. I would like to infuse the Fractal Capacitor to gain the extra infusion slot for AR. According to the wiki, performing the infusion would get rid of the Quiver skin. Does the transmutation splitter work with backpack skins? If not, would the recommendation be to make a new back item that’s infused and transmute my current backpack on it, so as not to lose the skin?

Yes. I used one over the weekend and got the skin, the back piece, and the gem all back.