FLT importer, Edge split modifier, Deformed mesh to Rvk script

If you’re not familiar with the “Deformed mesh to Rvk” script, it’s job is to add a shape key to the active object which has the same vertex data as a 2nd selected object. This is a very handy tool if you’ve had to import a series of similar models made in another modeling package and you want to have a single mesh with shape keys that look like the other imported models.

I’ve had great success with the script, but now I’m trying to import models with the FLT importer and these models are not working well with the script. The FLT models import with a parent-child hierarchy, which divides the model into sections (think arms, legs, torso, etc), and an Edge Split Modifier. Since my goal is shape key animation and not skeletal animation, the first thing I did with the imported models was to join them. The Edge Split modifier remained after joining.

The script isn’t working on the meshes because the number of vertices for all the models are different after import. I’m told they should be the same for each file. Why does the FLT importer add this modifier? Is it possible that the FLT importer is creating the wrong number of vertices or that the modifier is throwing off the number of vertices?