Normally, there wouldn't be too much of a difference. But 28% of a grain bill being flaked wheat is a lot. Are you brewing a wit? First off, the taste/mouthfeel will be a little different. Flaked wheat has more proteins and usually gives more haze, bigger mouthfeel, and wheatier flavor. That said, with more than a quarter of your grain bill being Flaked wheat, you should have probably planned on doing a cereal mash and/or be prepared for a slow/stuck sparge. Malted wheat won't be as big a problem, and since it's malted, it can convert itself. Flaked wheat would be relying on the enzymes of the other grains.
All said, I'd go ahead and brew. It will be a little different, but should still taste delicious.