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1. make sure you have Normals ticked on your OBJ export options in Maya, also check your Import options in zbrush. You can flip normals in Zbrush using Display properties > flip
2. If you are using Zmapper to bake your nmap then make sure you are using a Maya preset (they come with zmapper) alternatively flip your green channel in the nmap to get it working right in Maya
3. best thing to do is repair it in Maya and take it back into zbrush, I've never tried repairing holes in zbrush
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