Solution : https://service.sap.com/sap/support/notes/663240 (SAP Service marketplace login required)
Key words : 
application group ->additional components -> upgrade tools -> corrections, sap web application server release 6, 40 -> #os independentor directly athttp, _app=00200682500000001943& _event=disphier&header=, file <putdir>/bin/toolfix_stamp, fix_<product>_<version>, upgrade control program displays, sap service marketplace, sap service marketplacearea, delivered cd set
Related Notes : 
       
| 885955 | Language content in DDIC import not imported (Upg 640/700) | 
| 876198 | Several delete/activate actions during import | 
| 788623 | Additions to upgrade on SAP SRM Server 5.0 SR1 | 
| 788218 | Add. info. on upgrading to SAP ERP Central Component 5.0 SR1 | 
| 780985 | No versions are created in the shadow system | 
| 775047 | Add. info. on upgrading to SAP Web AS 6.40 SR1 | 
| 716377 | Problem analysis in the upgrade: SPACECHK phases | 
| 693397 | Prephase activities for SRM upgrade (Version 4.0 or higher) | 
| 689574 | Add. info. on upgrading to SAP ERP Central Component 5.00 | 
| 684406 | Additional information on upgrading to SAP SCM 4.1 | 
| 670330 | Objects from comparison transports displayed in SPAU | 
| 669656 | Additional info about upgrade to SAP Web AS 6.40 MaxDB | 
| 663258 | Corrections for R3up version 640 | 
| 661640 | Add. info. on upgrading to SAP Web AS 6.40 | 
| 661252 | DB2-z/OS: Additions upgrade to Basis 6.40 | 
| 623723 | Upgrade: Application-specific problems | 
| 522711 | Corrections for upgrade to Basis 620 |