There are some red windows on the 737 and the CS-300 as well. Why are they painted red?
A red/orange color is typically used to denote flight test instrumentation. Indeed, these windows do contain such instrumentation. Below you can see a similar window on a 747-8I flight test aircraft (note the 7th window from the nose):
And the corresponding inside view:
The aircrafts shown above are test aircraft and the windows are blanked for mounting test instrument. The image below shows the inside of Bombardier C-series test aircraft, which shows the mounting of test equipment.
Image from airwaysnews.com
Also, the screengrab below from this video about C series testing shows the interior of the C series test aircraft with blanked windows with attached instrumentation.
Also, see this thread that discusses about the same thing.