moved to the scripting forum...
This solution requires two scripts: the "batchconvert" script from Peter Kahrel; and another script that needs to be created from scratch.
The batch convert script will allow many indesign files to be opened at once and either saved back as indesign files or exported to one of many formats. Read this for more info: http://indesignsecrets.com/creating-batch-pdfs.php
That said, the script also allows other scripts to be run prior to an export/save. This is where the following script needs to be created (this example takes the colour PANTONE 295 C and makes it spot again)
app.activeDocument.inks.item("PANTONE 295 C").convertToProcess = false;
In the OP's instance, replace the color "PANTONE 295 C" with an appropriate color, and duplicate the line and repeat for however many colors need to be converted to back to spot. Save the script and then when using the batchconvert script, call upon the script created above in the "run a script" portion of the batchconvert dialog box.
Wow, this works perfect.