Solution : https://service.sap.com/sap/support/notes/606417 (SAP Service marketplace login required)
Key words : 
correction instructions contained, rename double entries, create unique index, duplicate keys reason, unique index, duplicate keys, smofrqjd~001 index, table contents, smofrqhd table, bbpcrm server
Related Notes : 
       
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| 961511 | Add. info.: Upgrade to SAP CRM 5.0 SR2 ABAP | 
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| 826488 | Enhancements to upgrade on SAP CRM 5.0 ABAP | 
| 737800 | Enhancements to upgrade on SAP CRM 4.0 SR1 | 
| 607691 | Preparing table SMOFRQHD for upgrade | 
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