Welcome to FT!

So you accepted a full refund from JetBlue and booked new ticket with QR? Rather than doing this I would have challenged JetBlue removing your DOH to Uganda flight from the itinerary. Once ticketed it is really not your problem if JetBlue stops offering a codeshare flight for DOH-Uganda. JetBlue can just ask QR to ticket it if for some reason JetBlue is not able to ticket is anymore. You were way too gentle with JetBlue here, but if already cancelled and refunded, there is nothing you can do.

To your Q: No this is not common; I would say it is extremely rare for codeshare partner to cancel tickets already issued with the reference that the codeshare agreement has ceased for the flight.

Rest assured that you will travel with QR to Uganda without any risks of the ticket being cancelled.