I'm a bit confused as to why you would need to remove them from the original cr2 - unless you saved it with the redundant materials and need to recover it. In that case you could probably remove them, though to be 100% safe, I'd probably just install her to a temp folder and grab the original.

If this is like Dave's Posette V3 and other remaps I've used, the Terai Yuki2 V3 cr2 is pointing to an entirely different .obj that was probably extracted from an encoded .rte or ,pcf (Mover) file. Use the remapped .cr2 for V3 maps and the original for TY2 maps - they are independent. Hopefully DPH will be along shortly with any corrections or contradictions.  He'll get you sorted out.

"Democracy is a pathetic belief in the collective wisdom of individual ignorance." - H. L. Mencken