I replaced our skylight a few weeks ago. It also was a 2-piece lexan with a mottled clear inner and smoke outer. With a lot of scraping I was able to separate them but then a heavy wind gust took the inner liner away. It's easier to separate while the inner is still glued down.
I was able to duplicate it using a clear Icon Technologies 4" bubble inner and a Specialty Recreation 6" bubble smoke outer. It turned out very nice with less than 1" separating the two lenses.
Our skylight is the Neo Angle 30" x 13" opening (16" x 34" outer measurment).
Make sure you use the proper Sealant as most RV roof sealants are petroleum based and will eventually crack the Lexan.
Surebond SB140 sealant. I ordered 2 tubes but 1 was enough.
https://www.amazon.com/gp/product/B0...?ie=UTF8&psc=1
Installing a new skylight
http://www.irv2.com/forums/f115/installing-a-new-skylight-392007.html
Hope this helps.