Setting document title when using collect option

I am converting a large number of documents from an old software package to PDF.  The software gives the files meaningless names ie:(CCI01590) that I need to change to the actual title prior to conversion.  The problem is, when I click on 'Wait - collect' it uses the title from the file and not what I type into the document title box.  Is there a way to enter the title I want for the file when using the wait option?  I would really hate to have to print one by one and wait for the conversion since there are several thousand of these silly files to convert.