I would say (as would you, I suspect) that there is certainly a risk, yes. However, using the car for anything presents a risk and you need the MOT, so what is your other option? Can you leave it with the garage until the flywheel is done, then MOT it?

So the question is - will the high revs that are done for the emissions test risk disturbing the flywheel? Many thanks.

With a failing DMF probably no greater a risk compared to driving the car especially as most recentish VAG diesel cars have a rev limiter when a car is stationary. It's worth taking for an MOT before doing the DMF to make sure the test doesn't throw another major issue.