Changes to the LDAP server can only be made in MetaDirectoryServer.XML if a change has already been made to the LDAP server via the MetaDirectory administrator.
To do this, you can call the MetaDirectory Administrator once, make a change to the LDAP server there, apply the setting, and then change the setting back and apply it again. Only then can you successfully change the NonPagedLimit value.
Example for changing a setting e.g. change "Default display name as" or disable "Deliver contacts with images".