Not rewriting the firmware: if Leica made it open source, I would have liked to. I'm not up to reverse engineering it...So you’re talking about rewriting the firmware? That would be amazing! As for the sensor I’m not sure if it’s a failure or possibly a dirty connection, in all the excitement I forgot to clean the contacts before reattaching the cable so I’ll the mainboard and give everything a quick cleaning and see if that helps. How do you want me to send over the test shots?
What I do for my files: I have software that opens all of the DNG files in a directory, reads them in, applies corrections, and writes them back out. The .exe file is small enough to copy onto the SD card once it is inserted into the computer, apply the corrections there. Better yet- copy the DNG files to your computer then run it. The "GAMMA" code reads in M Monochrom DNG files, applies a curve, changes the pixels values to 16 bits (instead of 14-bits) and adjusts the parameters in the DNG header. I'm "thinking out loud" that a similar correction could be applied to the RGB values in your DNG file to bring the values in line with the older color balance. "It's worth looking at" category. Essentially applying the difference in the two spectral responses.
What would be good: If you have a color test chart, take some pictures of it with the sensor before and after changing the cover glass. Use the same lighting, lens, etc- so that the only variable was the transmission of the cover glass. Do this under dim light and under bright light, but do not saturate the test image. The "first thought" would be to apply a correction to bring the new image back to the values of the old image.