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What workflow? ... Some people so much get used to use jpg format that they just flatern everything even without any actual need.

Don't knowing about details i can say how i handle that kind of problem.

First of all trying to work with TIFF or PSD (windows usually don't want to show thumbnail of it so i preffer TIFF).

With TIFF can save everthing (almost) all layers, all adjusments layers and so and on and what is very important for me it supports transparancy so there's almost no reason to make complicate and sharp path. And all flaterning is done by other soft when its come to output (for my case Indesign generate printable PDF).

If your guy HAVE to flatern it then only sugestion is make your own TIFF copy it will cost a very large amount of memory but now it's relativy cheap.