Running facetize I get this error:
nmg_ck_lu_orientation() loop orientation flags do not match geometry
What does this mean and how do I fix it?
It means that something unexpected was encountered during the facetization process. That failure can be completely benign and ignored, or it could indicate a modeling error (e.g., infinitely thin adjacent faces), or it could be a simple bug. It's hard to say without seeing the geometry in question.
If you feel it's a bug, please do file a bug report at https://sourceforge.net/tracker/?func=add&group_id=105292&atid=640802
It can't be completely benign, as facetize never writes the output file. I did fond a workaround, though. In an attempt to speed up the facetize process, I reordered the unions of the final combination. In particular, I placed the small objects first and the large objects last. This did speed up the facetize command considerably, and it also fixed the error!
Glad you found a workaround. The order of operations can definitely have a big impact on whether tessellation succeeds and how fast it tessellates as the mesh verification is performed at each step along the way and is expensive.