Who changed your ticket? The agent or QR? If you were issued a valid e-ticket for the QR routing (not a confirmation, but an e-ticket receipt), it should not be an issue for you to be reissued into that. It strikes me that the TA may have changed your ticket by jumping the gun and not asking you first. If that is the case, QR may well charge to make a further change and that cost is, of course, the TA's problem to cover.

I think that you need to dig deeper with the agent as to how all of this happened and to ask to see the messaging behind the change. When you are told that it is all in codes you won't understand, don't let that deter you.

Another approach is to call the TA and have them patch you in with QR so that you can participate in the call (or better yet, you do the patching.