Solution : https://service.sap.com/sap/support/notes/650291 (SAP Service marketplace login required)
Key words : 
phase toolfix_chkupgrade correction packagethe upgrade correction package fix_scm401, directory /usr/sap/putplease check note 522711, rule-based availability check, upgrade correction package, tmc1tboth standard customizing entries, missing table contents retroactively, report /sapcn1/cust_indx_to_cn1 manually, upgrade phase toolfix_chk, customer-specific data, simple display errors
Related Notes : 
       
| 1647834 | Loss of data during upgrade: /SAPCN1/T682I | 
| 826093 | Add. info. on upgrading to SAP SCM 5.0 ABAP | 
| 684406 | Additional information on upgrading to SAP SCM 4.1 | 
| 650310 | XPRA /SAPCN1/CUST_INDX_TO_CN1 did not convert any data | 
| 603852 | Additional information about upgrading to SAP SCM 4.0 | 
| 522711 | Corrections for upgrade to Basis 620 |