After creating a BW System copy both source systems (old and new source system) exist in different tables (e.g. table RSDS). Therefore, BDLS cannot convert those tables .
Example: Table RSDS
BDLS will not be able to convert this table from PROD --> DEV as it contains two entries with the same key. This is not allowed.
BDLS either converts the whole column or none of the column entries. Also refer to the following link BDLS - Logical system name conversion.
SAP NetWeaver All versions
BDLS; BW system copy , KBA , BW-WHM-DST-SRC , Source Systems , How To
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