The files names for the PDF files cannot be edited, however, there is a work around for this issue where there is an underscore in the file name:
Export the fund statements normally, and before opening Word to merge the statement data into the template, open the file "fndstat.txt" in Excel, look for the columns\data that shows the underscore. Change the values there and the save that txt file and then merge into Word.
For the fund statement export, if you have that set to automatically launch Word, you will have to uncheck that checkbox and not automatically launch Word, then just export the data files out and edit as described above and then open Word and merge using the "fndstat.txt" file as the data source as you would for normal Word merge.