It's very hard to know what's going on based on just a description. Can you try and post a small example? You can use the reprex guide
A reprex consists of the minimal code and data needed to recreate the issue/question you're having. You can find instructions how to build and share one here:
Just to be sure: The PDF you're trying to write to is not opened on your computer right? Because often times these files get locked when opened, and no other software can overwrite it while this is the case.