So I fitted my new secondary today and took some flats, I had taken some before the transplant and not moved the focuser inbetween. The light box was on the same setting and the camera settings were not changed.
The average pixel values went from 13000 to 14500 a gain of around 11%
Before I started this I theorised a gain of 18% because my area of obstruction was going up by 7% but I should be getting the 100% rays now instead of the 75%. Needless to say I am stoked with an 11% gain especially when I am getting less vignetting aswell.