Hi Tharindu,
This functionality is designed with the intention that all Parts must be included. The delete option was removed as an internal correction in Apps 10 from Quality Basic Data tabs Site, Part and Part/Site to avoid errors in the setup for this parameters.
If a user, for instance, changes a setting on Site, this setting will then be propagated to all Parts and all Parts / Site as well.
But if a Part or Part / Site had been removed from this client, this part would not get the correct setting and, for instance, a mandatory setting on Site could be bypassed