Thanks to the help provided by @mkl Here we were able to figure out how to monkey patch the pdf binary. So then I just need to be able to do so in CF. Since reading the file in as a text file causes problems due to character encoding I was able to do this.
Identify the text to change in the binary. This is what @mkl helped my with. The problem text is "/K true" which is telling the PDF to use knockout groups which I'm sure makes sense to PDF experts but is total Greek to me.
Read the pdf into coldfusion as a binary
<cffile action="readbinary" file="#inputPath#" variable="input">
Encode the binary bytearray to Hex
<cfset temp=BinaryEncode(input,"Hex")>
Remove the, now hex, string I want removed
<cfset temp2 = ReplaceNoCase(temp,"2F4B2074727565","","All")><!--- 2F4B2074727565 is HEX for /K true --->
Decode the Hex back into a bytearray
<cfset output = BinaryDecode(temp2,"Hex")>
Write the output file to the file system
<cffile action="write" file="#outputPath#" output="#output#" nameconflict="overwrite">
Now you have a PDF that looks like expected. The problem is that there is something wrong with it. If I open it, do nothing, and close it I'm prompted to save. If I save it, I no longer have an issue. I figured that a CFPDF merge operation would do basically this without requiring a user to do something so I added this final step.
- Resave the pdf with the merge command
<cfpdf action="merge" source="#outputPath#" destination="outputPath2" pages="1" overwrite="yes">