This may just come down to knowing how the software handles references, and being diligent in post process clean-up.
When you add the pdf as a reference, PDM will treat it no different than if it was a part in an assembly. The files you copy will still maintain a reference to the files you don't copy. This is a great feature when you want to make a new assy which is almost identical to the original. But, in your case this has become a hindrance.
You may simply have to remove the reference manually after you create the new file(s). This will become part of your standard work process until a better solution is developed.
I would also submit an Enhancement Request (ER) to SW asking them to add something like a "Break Reference" column to the Copy Tree tool. If you do submit an ER, post it here so that myself and others can support it.