Upgrade E6500 CPU to QX9300?

The M4400's standard GPU is better than the E6500's best one. You'll also need a new heatsink, AC adapter, etc, to handle the new requirements.

This is exactly what happened when I tried a Q9100 in my E6400. It seems the Latitudes are just not compatible with quad cores.

 

Correct, you would only be out the value of the E6500's mainboard if you bricked it. OTOH, I bet you could get at least $150 for the E6500 mainboard on eBay (so long as it was still functioning) which would cover 50% of the cost of a refurbed M4400 mainboard. I guess if you don't care about the money go for it.

As stated before chip in the M4400 is better than the nvidia chip in the E6500. You cannot exchange the GPU in these models... when you buy the M4400 motherboard it will have the better graphics included (obviously).

Yup, you would just toast the mainboard. Your RAM, HDD, CPU, LCD, etc (essentially everything attached to the mainboard by a cable or connector) should be fine if the flash didn't work.