I just had great success with the following edits to this code. Thanks for sharing it. I also was able to change it to export JPEGs.I'm attaching my Python script.#DDP: Set Definition Query on a secondary index 
 #Variables that need to be set by user:
 #mxdpath = r'C:\Users\Test.mxd' # string
 #outputfolder = 'PDFFolder' # string
 #namefield = 'THE FIELD CONTAINING THE NAME OF THE RESULTING PDF FILE' #string
 #queryfield = 'THE FIELD CONTAINING THE VALUE FOR THE DESIRED QUERY' #string
 #layers = ['LIST','OF','LAYERS'] # list ('Layer1_UpdateQuery', 'Layer2_UpdateQuery', 'etc')
#Import Modules
import arcpy, os
# Set Variables
mxdpath = r'D:\arcgis\Samples\DDP_Index2.mxd' # string
outputfolder = 'D:\PDF' # string
namefield = 'FIPS' # string
queryfield = 'STATE_NAME' # string
layers = ['CountySel_FIPS'] # list
mxd = arcpy.mapping.MapDocument(mxdpath)
# Start Loop through Data Driven Pages
for pageNum in range(1, mxd.dataDrivenPages.pageCount + 1):
    mxd.dataDrivenPages.currentPageID = pageNum # set the current page
    pageName = mxd.dataDrivenPages.pageRow.getValue(namefield) # get the pageName
    pageName += '.pdf' # add '.pdf' extension for file name
    pdf = os.path.join(outputfolder, pageName) # add pageName to output folder to get full output path
    # Start Loop through all layers of mxd file
    for lyr in arcpy.mapping.ListLayers(mxd): # for every layer in mxd's Layer List
            if lyr.name in layers: # if layer name in user input list above
                #value = mxd.DataDrivenPages.pageRow.getValue(queryfield) # get value of query field
                value = mxd.dataDrivenPages.pageRow.getValue(queryfield)
                print value
                if lyr.definitionQuery == True: # if a definitionQuery Exsts...
                    query = lyr.definitionQuery + "AND" + queryfield + "=" + "\"" + value + "\"" # Add new to old
                else:
                    query = queryfield + "=" + "\"" + value + "\"" # else create a new query
                    lyr.definitionQuery = query # set the layers defintionQuery
            else:
                print 'Next' # else print next, this isn't necassary, but its a good place holder
    print pageName
    arcpy.mapping.ExportToPDF(mxd, pdf) # export the current Page to pdf
del mxd, lyr, pageName, pageNum, query, value