Hey there!
It looks like you have a couple of different things going on here.
It’s hard to say for sure without seeing your file, but here’s what I think might be causing the issues:
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Some of your subtools might have ‘Dynamic’ subdivisions on. Make sure you apply dynamic subdivision levels before merging so that you don’t end up losing your subdivision information when you merge. Click “Subtool” > “All High” before merging to make sure you’re merging at the highest subdivision level for every subtool.
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it looks like a bunch of your subtools have flipped normals. If you go into ‘Display Properties’ on one of the subtools that is doing weird things (try his kneecaps), then you’ll probably notice that “Double” is enabled. Disabling double will show what you see when you merge it. To fix the error, disable double, then click flip. This will switch your normal direction, and stop the mesh from displaying inside-out.
Hopefully changing these fixes it! If not, I’m sure we can figure it out.
Good luck!