So first, let me apologize for going on and on about metrology issues, but with this kind of measurement they are important.
I did the math, and there might not be an issue with the differential measurement. With an ideal 10M resistor across the circuit, the Q will drop by roughly 10%, and a 1% linearity error would create roughly a 10% measurement error. So you would have a possible 15% error on the initial measurement plus another 10% for a total error of 25%. I don't know if a 1% linearity error is in fact reasonable, but it at least seems reasonable.
Change the scenario to a 100M resistor, and the Q will only change by 1%. With such a small change in Q, the linearity error would also be less, so again perhaps adding only a 10% error to the net result again. At this point however, resolution and repeatability become more important -- the change in Q would be from say 1000 to 990, and the difference between a reading of 990 and 991 represents a 10% change in the answer.
This is in addition to the issues folks have brought up with the 10M test resistor.
The inductor should be looked at too. Does it have a closed magnetic circuit so that external fields are minimal? If it's an open circuit such as an air core coil, the Q can be altered significantly by nearby objects, so that would need to be managed carefully. It may not take much to alter losses in the inductor by a few percent. It would be easy to explore that issue using the Q meter.
Suffice it to say this is a very challenging task!