To be clear, there are 2 problems. First the problem with the nested subsheets,
2 sheets A and B
each containing 4 identical sub sheets. Every sub sheet has an R and LED.
Here I used replicate layout one time with subsheets as reference.
Than I manually dragged the sets belonging to sheet_A into a good position.
(unrelated, but the tracks with the vias arent copied)
I want to mirror this layout for the parts of sheet B as well so I’ll use replicate layout a 2nd time with now the main sheet as reference.
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And this does work.
However, this mesh is usually a problem when you have much footprints. So I removed the board and I redid the board, but this time I checked ‘group layouts’
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That also works. But now the last part. Like before I want to duplicate the layout of sheet A to sheet B. So I enter one of the 4 groups of a component in A. I select one of the footprints and I try to use the replicate layout again. Only this time this message appears
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While typing this post, I came up with this workaround.
I manually placed 4 groups into their final position. Therefor I have no need for them being in groups, so I deleted all groups in sight. Than I retried the plugin and…
This seem to work. I did notice a few tracks floating but that may be me screwing around things.
I think this workaround (= ungrouping groups after dragging them in final position) is completely workable IMO.
Back to the other problem.
I rotated one footprint and I tried to replicate the layout again. I checked group layout again but onfotunately the group, which I just manually deleted… still seems to exist.
I looked into the board file with an editor and I saw no groups. So I closed and re-opened the board editor.
And now it does work.
So I think no actions have to be taken.
There is however one smaller 3rd issue. The floating tracks are a recurring theme. I can trigger it fairly simple by using Ctrl-Z after I used the plugin.
This could be annoying, if you replicate something and you have made a mistake or you need to add something.
Regards 
Bas
test.zip (23.9 KB)