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Flattening a PDF through Webscript

I have come across an issue on a site I developed. I allow people to upload their PDFs to our site and we modify them with PDF to SWF to show the PDF content in our application. From our application we print the SWF. The problem I am finding is that some of the PDFs when uploaded have many layers. When it finally prints it does not handle transparencies. I have found that if I flatten the PDF before uploading, the process works perfect.

What I need to do is modify the PDF after uploading through scripting the modification through PHP. Does anyone know of a command line PDF tool that will allow me to flatten a PDF. I currently use swf2pdf and pdftp but these tools do not allow me to flatten the PDF.

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Vadim Rapp
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