Just to update you on this, too: I took out a Developer Technical Support ticket with Apple’s engineers on this, to ask if there was any way to remove colour profiles from PDF files using the Cocoa frameworks (that is, the Apple technologies available to developers). An engineer replied to say that there is currently no way of doing this - all of Apple’s PDF technologies embed colour profiles with no way of removing them. This means that I am not able to add a fix for this to a Scrivener update (I have filed an enhancement request with Apple asking for this feature, but it’s unlikely it will ever be implemented).
So for the foreseeable future, the only way of fixing up PDF files for IngramSpark is to post-process them in Adobe Acrobat Pro, as described above by RonSmithMD. (Given that the PDF format was Adobe’s creation, I suppose it’s not surprising that some PDF features are only attainable using their tools.)
All the best,
Keith