I'm having issues with this with XSI, it seems like it always compresses it down to 1 UV channel when I export.
OBJ is 1 UV set only. FBX or Collada work with multiple UV sets. You might have to set the material to use both sets before exporting, and possibly try an older version of crosswalk.
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really? the .xsi isn't working.
What if I have the the UV's already set up? is there anyway to merge without loosing them?