Can I convert a Contour Canopy (with windows) into a camper/tent setup later on?

The main supported modification is adding a roof top tent on top of the canopy. Modifying the canopy itself in other ways isn't something we can advise on and would void the warranty. If you want a canopy that converts between a canopy and a tent, the Alu-Cab ModCap is built for that — it's modular and can be used as a canopy or transitioned into a 2- or 4-person tent.