Force NTFS permissions inheritance for newly created files
As a temporary solution to the problem I created a .bat with
icacls "folder_path*" /inheritance:e
and have put that in Task Scheduler.
If anybody else comes to a better idea, please post it in the answers.
EDIT: The problem was that the PDF file was first created in %appdata% folder and then it would get moved in the custom folder on the same drive and therefore would keep the original permissions it had in the %appdata% folder.
I created a new folder on another drive and the file inherits the permissions of the folder where it is saved(since moving on another drive is actually first copying and then deleting the original file).