Batch JavaScript Fails to Save PDF from XDP

I generated hundreds of XDP files from a database query and need to merge them with a PDF template. Using Acrobat Pro 8 interactively allows me to do this by opening the file and then saving it, but I need to do this for hundreds of files.
So, I created a batch script that would run on all files in a folder and it does run on the XDP file but the form data is not populated in the PDF. Batch mode seems to be different than Interactive mode when dealing with xdp files.
Can I make this batch script merge the xdp form data into the PDFs? Is there a different or better way to do this?
Thanks.
Peter
In addition to just letting the batch process save the files, I also tried to save from a JavaScript "command" in the batch process.
/* Save the document */
app.execMenuItem("save");

I tried that first (without the save), but the resulting PDF had no form data from the XDP. That's when I added the save.
The merging seems to fail when run from batch, but it works fine when I open and then save the file in Acrobat Pro or Reader.
Is there a command in the batch processing that is necessary to move the data from the XDP to the resulting PDF? Will the proper Save command do the trick? [I left work early due to our snow so I can't try this myself.]
--Peter

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