I'm afraid it probably won't be OK to make such a large change to the thrust line.

You don't give details, but it's very likely there's an extension available for your muffler for this very problem, which is a much better solution. I would strongly suggest you look into this, and avoid making such a significant change to the design of the model.

You could probably trim out the effects of this change in the designed thrust line, when flying in a straight line, but it's almost bound to make a difference in some unpredictable part of the flight.

David C.