Solution : https://service.sap.com/sap/support/notes/63037 (SAP Service marketplace login required)
Key words : 
command wrklib r3<sid><pkgkind>, sap namespace 'r3<sid>', deleting individual sql packages, 'r3<sid> ' manually, ptf cover letter, i5/os reason, individual sql statements, operating system upgrade, deleting sql packages, relevant package library
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