Hi Ajinkya,
During product change process from CRM keep break point in CRM 'CRM_UPLOAD_FILL_DATA' method of badi implementation of ECRM_UPLOAD badi.In debug remove the container value for the installation operands which are not updated during the process,Check it should not make change time slice for these operands in isu. if by this way no changes are made on those operand, you can code that way to resolve your issue.
Thanks
Ayan