Hey there,
I don’t know if you still have this problem, but after some trials and errors I guess I found out what’s causing the problem. It happened to me too…
I’m modelling a character with multiple subtools, all have UVs and follow the same principle (low to high poly, at the moment I’ve deleted some of the high-res levels and I’m at SubD 4).
I’ve managed to merged almost all the subtools without having problems, but there are two substools that are those that are causing the problem.
Try to follow these steps:
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If you have multiple subtools merged correctly with subdivisions preserved, try this: Geometry > Meshintegrity > Check Mesh Integrity. It should say to you “Mesh integrity test completed successfully”.
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Try now to do it on a subtools that you think is causing the problem, it should tells you that there is error in the mesh. To me it says “The mesh contains 1156 out-of-bounds UV coordinates. The mesh contains 576 edges that are shared by more than two polygons”.
This is what you have to fixed in order to proceed and merged all the subtools correctly.
Hope it helps,
It used to drove me crazy not understanding what was causing the problem.
All the best with you project!
Gabriel