>What its the effect of mixing in one brood box, combs on 4.9mm foundation with combs
on 5.4mm foundation?  Does it matter?

I have some PF-100's mixed with foundationless frames. Bees build the foundationless out before the plastic. Most cells are small, 5.1 -5.2 in the center of the frame and get larger toward the edges, sometimes larger than 5.5. I don't find any problem with this and bees seem to do well with it. Plastic frames make the foundationless much straighter. Of course all the plastic are 4.9.

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