Blending works with the polygon vertices. For the process to work, you need to have blend shapes and a blend target that are identically numbered. I have read that Maya 8 lets you do blends with dissimiliar models but I've never tried it. If your bound model and your newly imported model are having problems with blends then they don't have the same numbering. Maybe you added more edge loops to your bound model... I can tell you that if you export your model as an obj then import it back into Maya, the vertices numbering will be changed. I don't know if you are importing an obj copy of your model or if you are importing the Maya Binary (.mb) file but only the .mb will work, assuming the vertices between the bound model and the imported model are the same.

As far as unbinding your model. You should turn your IKs off then return your model to the bind pose. If you don't know how to get back to the bind pose then you probably didn't rig your model correctly. It should be as easy as setting your control objects' rotation and translation values back to zero.