As I wrote before: I have to process the stream. I can't create a MagickImage because of performance issue.Why don't you use Magick.NET to remove some of the application markers?
I fixed that problem in a following way:
before saving image I use Strip() method to remove all application markers and after that add only needed profiles in the correct order.
So I don't need to change code that processing the stream.
Looks like it works correctly.