I have read that these types of files cannot change between update versions, but this does not make sense to me. A patch or "tiny update" should be able to process these files and update them.
I'm not sure where you read that, but wyBuild can handle *all* files (exes, pdfs, dlls, word documents, images, etc., etc., etc.). It doesn't care what's inside the files.
This problems is almost always caused by the version in wyBuild that represents your old version doesn't match the version you're including with your installer and that's being delivered to your users.
Make sure the old pdf in your V! folder matches the pdf file on the customer's computer. Make sure the customer didn't modify the PDF, and make sure no other program modified the PDF on the target computer.
A good place to start is the step-by-step walkthrough.
Am I doing something wrong or am I missing the fact that wyBuild only works for exe, dll and the like and not support files (which for me change frequently without changing the exe)?
wyBuild supports all files. I'm not sure where you read otherwise.
Tell me if this helps.