The scenario: You have a project workspace linked to a project That workspace has a custom document library/list or Item that requires limited user access The permissions for the document library are not inherited from the parent site Users for this document library/list are added individually The action Customer permissions are changed in PWA User Sync kicks off and re-syncs the users permissions The outcome The user permissions are removed and re-added to the site as expected Any "unique" user level permissions on the site are removed (ie if you have added additional "contributor" access as well as the Microsoft Office Project Server group permissions, etc) The users permissions on the list/item that do no inherit from the site are also removed but are not re-added It appears that the user synchronisation can remove all permissions from the site, lists and items including those where permissions are not inherited, but can only add site level and inherited permissi