Hi Sunil,
Data discrepancy between physical and logical inventory is always a pain for any service provider. Telcordia's Granite Inventory system has a module called discovery that claims to resolve these discrepancies without much manual intervention. I'm not sure how effective this is, as I don't have much expertise on usage of Granite.
But few companies build proprietary applications to identify these discrepancies. Data from the inventory system (logical) and network elements (Switch, router, DCS) are compared to generate a discrepancy report. These problems are then manually resolved.
Regards,
Patrick