Uh, you should never really have to do anything manually in the .ma file... in fact that sounds like a really bad idea to me unless you really know what you're doing (and even then, why not just do the same thing in Maya?!). For example if there are hidden nodes which have been left around from previous operations for…
There may also be hidden mesh data, if you've copied or duplicated, or hidden things. I've had that sort of thing before. Open up hypergraph and check options->display->Hidden Nodes. There may be one or more older copies of your high poly or something that are just hidden, or disconnected from a proper output/display node…
you can try the "show dag only" in your outliner... But probably hidden nodes... If you can save your file as *.ma file, open it with textpad and do a research with "lightlinker" on something like that... Sometimes some nodes are duplicated in the *.ma file file, and nobdy know why. The optimize scene size or clean history…