Why would a copilot's window be shaded/covered?
Aircraft flight decks can become very warm at times and pilots will always try their best to avoid letting the sun add any additional heat. 

Most aircraft have sun visors or sun screens as part of the flight deck equipment. These are usually a clip-on design or pull-shade design. Both types are translucent and can be left in place for all phases of flight. 

Many pilots will also bring their own temporary sun shades to use in the flight deck. Theses can be translucent or opaque. Many pilots even use their charts as temporary make-shift shades while parked at a gate in the blaring sun. 

Since you described them as reflective covers, I suspect what you saw may have been some kind of temporary shade supplied by the company. They would not be used on the forward windscreen so they would be safe to use during taxiing. 

Here are some examples of a pull shade being used in an ATR 72.




Here is an example of what looks like a reflective shade.