We have a file that we need to merge verts on, but the file is too big and crashes if we open it.  I know a few non scripted ways around this, but i am purely interested if there is a way to use mel/python to run merge verts on the file without actually opening it, from either Maya or the Cmd prompt.

To edit a maya Binary file you have to use Maya. you can use the batchMaya, that is a maya without a UI, but it still is maya. If its a Maya Ascii file you can edit it as text but the file size is a bit bigger.