Solution : https://service.sap.com/sap/support/notes/109059 (SAP Service marketplace login required)
Key words : 
directory ~ftp/general/r3server/patches/rel40b/, ~ftp/general/r3server/patches/rel40b/, additional key words r3trmcid r3trmcob, directory /usr/sap/put/exe, directories /usr/sap/put/exe, directory /usr/sap/put/tools, destroyed matchcode ids/matchcode objects, transport object r3tr mcid xxxxy, /usr/sap/put/tools, customer-specific matchcode ids
Related Notes : 
       
| 147439 | IS-H: matchcode search delivers too many entries | 
| 128589 | Upgrade to 4.0B/4.5A destroys customer variants | 
| 99379 | Additional Info: Upgrading to 4.0B DB2/400 | 
| 91709 | Addition upgrade to 4.0B | 
| 19466 | Downloading SAP kernel patches |