Painting clear finish over both flat and semi gloss

It may take a few coats but they will end up with the same sheen. Use light coats barely wet so the undercoats don't soften and mix with your top coat.

Pete

I have done this successfully on some models.     I don't  think  you can hurt is to try.    Lately most paints I use have been flat since I can't get gloss.    So I gloss coat to put the decals on and then after they are set and dry and bubbles taken care of, I overspray with satin or a dull coat and the parts that were flat and the parts gloss coated look the same to me.

This is all opinion you realize!

"I'm not asking if the colors will retain their original sheen, side the satin will obviously govern. Just wondering if there will be a difference in final appearance at all between the two. Trying to maintain a very subtle two-tone looking finish."

Theoretically once the clear-coat is applied the sheen will be consistent. In practice this is sometimes true and sometimes not, at least within the scope of my typical overcoat number - 2, 3 or 4. Past that I can't say. There can be subtle physical and even chemical interplay between two different original finishes and the clear overspray, it seems. Do it with patience and moderate coats; just don't be surprised if some sheen differences are persistent. It's usually slight, if apparent at all. 

(As W.C. Fields used to say: "if it first you don't succeed, try, try again. After that, give up - no use being a d**n fool about it".) 

If I understand your question correctly'. I would not use satin.  I would use flat clear coat from Krylon on the flat black:  And use Gloss Krylon/Rustoleum on the glossy black.  Of course you will have to mask with tape for a professional look.  I have done this many times on two tone cars.  The finished result will be what you are looking for.  Just spray lightly and from a one foot distance'....

I think most of you guys are misinterpreting my question, I actually desire to have a visible difference after the top coat.  I would like for the finished appearance to be a subtle 2-tone when it's all said an done.

@Quarter Gauger 48 has it right.  I was hoping to not have to mask anymore since it's a very tedious location and it would take a while.  Thought maybe all my masking work to separate the flat and gloss black coats would mean I wouldn't have to spend as much time and just spray a single overcoat.  

Sounds like I'm just gonna have to give it a whirl and see what happens.  

Jeff, if you have  a steady hand'... you can use a brush, and not mask.  Just spray the paint into a small container, probably 1/4 inch should do it for each application of the clear coats... Less tedious than the masking.... Good luck with the project... Let's see the finished results'...🧐