Hi Gustav, it's very difficult to figure anything about file import/export without being able to test with the actual file. If you want to keep it private you can e-mail it to me at moi@moi3d.com .
It could be something like the problem faces had a damaged trimming boundary from the beginning but it wasn't immediately apparent until after a round trip through .3dm format. But I don't currently have any examples of that over here so I can't really tell anything for sure without testing the actual problem file.
- Michael
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