Frankly, that looks complicated with an element of risk.
You are willing to spend 6+ more hours in DOH (i.e. arrive in London 6h later), spend a large number of avios (that you could use for a leisure trip), possibly have problems (including with your employer) for upgrading a 6.5h flight?
I assume that you will not check luggage. If you do, that is simply impossible.

To answer your questions in order:
1. The best/more legit way would be to simply upgrade QR9 from Y to J. I don't know which fare bucket your TA uses, but the cost would be from 20k to 40k avios (https://www.qatarairways.com/en/Priv...alculator.html). Now that QR also uses avios, it is trivial and instantaneous to transfer avios to QR program and back. The only question is whether there will be availability.

2. You cannot cancel your QR9 booking until you have flown the first segment, as it will also be cancelled. Actually, you will be issued your QR9 boarding pass in BKK, so that's really awkward. As long as you/TA don't claim a refund, you should not have to pay a no-show fee.

3. If you use the same FFP number for both bookings on the same day, QR might flag you. I have no idea whether QR does it, some airlines do.