In your compile settings click the “as is” box on prologue, acknowledgements, etc that you don’t want compile to label as chapters. That should prevent scrivener from labeling them so. That way you can have your cake and eat it too. 
In your compile settings click the “as is” box on prologue, acknowledgements, etc that you don’t want compile to label as chapters. That should prevent scrivener from labeling them so. That way you can have your cake and eat it too.