Hi Dean,
You can lock the access to the document down but you cannot change the actual PDF to have it flattened.
Configurations, File Cabinet, edit the file cabinet, Permissions, turn advanced button on.
Setup an index value profile with only the rights you want people to have. Then update your WF's to change the field(s) used in the security profile to the values used there.
Hope this helps!
Ross Lister
DW PS Team