I've been plagued by the mysterious "uv set with a mind of it's own" problem for quite some time now. I always back up my work with objs, but that really gets old and it's not that practical if you have a lot of objects.
I'm actually still using maya 2009, so does anyone know if maya still "forgets" uvs sometimes when you reopen the scene?
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I've been working with maya for 2-3 years and never come across what you describe.