Use the community commons DuplicateFileDocument. It will copy one filedocument into another filedocument.
Not sure what exactly you are trying to achieve - to replace the original pdf or merge the two pdf files. If the latter one, use DuplicateFileDocument as suggested by Ronald to copy the newly uploaded file to overwrite the original. If you want to merge them, use MergeMultiplePdfs java action. Both are available in the Community Commons module from the app store