Modeller, the 'error' is (and always is with 3D) small triangles, see images attached.
Metasequoia states the file is maximum ~8 units in length, so the smaller part is, in number terms, very small, and the small triangles are very very small, in computer number terms.
Basically pepakura is stripping out the small triangles, it probably told you some triangles were deleted so it could cope.
A x10 or x100 unit conversion would probably fix such problems, on export, because pepakura import isn't very good.
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