Got some more info from another person who previously debayered their sensor. He made two excellent points:
1. We could use
Astronomik MC-Klarglas as a high quality (and high cost) replacement glass. Multicoated, comes in various square sizes for different Canon DSLRs. I could not find the dimensions on the Astronomik website, it may need cutting to the right size.
2. The effect of glass on the optical path. If a glass is inserted in the optical path the distance to the sensor has to be lengthened.
"Typically this is referred to the Rule of 3rds, where for each 1mm of glass added to a optical path you will need to allow 1/3mm of extra path spacing. This can be critical with CCD and mono cmos cameras. So typically colour or narrowband filters will be say 2mm thick, and sensor windows that cover the sensor chamber are usually 1mm thick, so that is a combined 3mm of glass, therefore using the rule an extra 1mm of spacing is needed to ensure precise backfocus distance is maintained."
This is not a problem for everybody but, for example, if a field flattener is used, usually they require exact spacing to the sensor and extra glass can affect this. My flattener needs spacing to be within 0.5mm. The above example shows that the flattener will not work correctly unless 1mm is added to the optical path.
Also, when I was removing the glass with heat to do the debayering, at some stage it looked like something was "burning" on the glass. Perhaps this was the reflection coating?
I will check my mono camera in 2-3 days, once the clouds go away.