Remove doubles messing with textures

New to Blender, and this website so please bear with me.

It seems like I need to remove doubles on my model in order to apply an Armature without getting the Bone Heat Weighting error. Remove doubles works just fine for some models, however for other like this robe below it completely messes up the look. It looks normal before I remove doubles. Any ideas on how I could fix this?

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Remove doubles, reunwrap the faces that got jacked up.

Sorry dont have any other solutions.

The feature that may prevent this is currently being worked on I think