Here is the current situation. Have an ex-CAI AONE4, the last segments being LHR-DOH-AMM (16 hour transit in DOH) all on QR. I want to drop the DOH-AMM segment but not pay for a another re-route. Since I can end the trip anywhere in the ME, I would still have a valid routing.

I want to book a separate award ticket departing DOH on the same day as the scheduled DOH-AMM segment using QR for the award flight. I had an involutary reroute of DOH-CDG-LHR to DOH-LHR (no charge) but with a 25 hour stop in LHR. I'm not sure if I have used my 2 stopovers in continent of origin. Is this possible? I might switch the DOH-AMM to RJ to avoid this, but RJ & QR use Amedaus so it may not work. Suggestions?

Changing a transit to a stopover is considered a re-routing. Whether or not QR will allow you to short-check to DOH with a 16-hour transit, I have no first hand experience myself, but I would imagine a yes. You can then check-in to your new flight if you leave enough time. You might even still be eligible for the QR STPC package.

Just my two cents from my experience:

If the airline reroutes you they usually leave the original ticket untouched, just issue replacement coupons.
Also not using the last sector on a xONEx was never a problem friends of mine. Only potential issue could be short checking you luggage to DOH only, but with a long transit you have a good reason to need your luggage in DOH.
Another issue might be that you have two reservations on the same airline around the same time. Not sure how sophisticated the QR system is, but LH for example is able to automatically find these and then cancel one. No experience on QR. You might be safer not entering your frequent flyer information for your new flight or even booking a different airline for your last sector.