I replied to PBLNRAO Kiran.
I have solved my issue to a degree, by running a mel script.

//batchExportFBX.mel

//Get the folder with the animations to process
$folder = "C:/animations/SOURCE/";

//Get the files within that folder
$files = `getFileList -filespec "*.m*" 
                      -folder $folder`;

//check there are files in the folder
if ($files[0] == "") {
    error ("There are no animations in " + $folder + " folder!");
}                      
//Loop through each file in folder
for ($filename in $files){
    //Open file
    file -open -f -loadReferenceDepth "all"  ($folder+$filename);
    //RUN ExportFBX.mel on each file
    source "c:/Scripts/ExportFBX.mel";
}

I would prefer it to not have to run it through the script editor, as it would 
be more efficient to not open up maya at all, but I don't know how to do that. 
please help!
Thanks


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