Solution : https://service.sap.com/sap/support/notes/746476 (SAP Service marketplace login required)
Key words : 
information zum download von patches finden sie, sap service marketplace software center, /usr/sap/put/exe, r3trans version dated december 15, r3trans version dated june 15, corrected r3trans version, xtern_cnv upgrade phase, client-specific tables, corrected r3trans, exe directory
Related Notes : 
       
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| 420371 | Add. info on upgrading to Basis 4.6C SR2 (NDI upgrade) | 
| 401717 | Additional info on upgrading to SAP Web AS 6.10 (Basis) | 
| 390062 | Additional information about upgrading to 4.6C SR2 | 
| 335029 | Additions to the upgrade to Basis 4.6D (NDI Upgrade) | 
| 329622 | Additions: Upgrading to Basis 4.6C SR1 (NDI upgrade) | 
| 327285 | Additions to upgrade to 4.6C SR1 | 
| 19466 | Downloading SAP kernel patches |