I'm late to the conversation, but I had the same problem with populating a PDF form with data, saving that PDF, then flattening the PDF.
Here's how I solved it in CF9:
<cfset path = "#GetDirectoryFromPath(GetCurrentTemplatePath())#doc\">
<cfset srcFile = "template\myPDFtemplate.pdf">
<cfset destFile = "yourPDF.pdf">
<!--- Using NAME instead of DESTINATION tells Coldfusion to create PDF in memory --->
<cfpdfform action="populate" source="#path##srcFile#" name="#destFile#">
<cfpdfformparam name="field1" value="some value">
</cfpdfform>
<!--- Using the variable in the SOURCE tells Coldfusion to read PDF from memory --->
<cfpdf action="write" destination="#path##destFile#" source="#destFile#" flatten="yes" overwrite="yes" />
Hope this helps others.Mark