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The animations are seperate files from the mesh and texture. Depending on the options you chose, they may or may not have been copied into your clone file, but if they weren't, they will still be linked to the object.
So, if you just want the object to look different, but act the same way, you do not need to do any animations. If you are changing the mesh (GMDC), then you do need to use a method that supports joints. This can be done with the SMD format amd SimPE, using several 3D editors (3DS, XSI, MilkShape) or with the OBJ format, meshtool and several other 3D tools. There are plenty of posts and tutorials on retaining the animations, which just means the original joint structure is maintained.
<* Wes *>
If you like to say what you think, be sure you know which to do first.