Resolution:
In order to avoid any conflict in the RFC/BAPI schemas while downloadng schemas from different SAP Applications having SAP kernel version, you can download the IDoc/RFC/BAPI schemas from the latest SAP application to the custom folder.

SAP Adapter allows the user to download the schemas from SAP in different folders so that the schemas are independant of each other.

Please follow the below steps to download IDoc/RFC/BAPI schema to the custom folder

1) Click on R/3 Adapter Configuration-> Adapter Services folder.
2) In ‘Custom Folder’ field, please give the value for the custom folder (say SAP_640)
3) Then click on IDoc/RFC/BAPI  services and do a refresh schema.
4) And check whether the schema has been created under the custom folder SAP_640 folder

This feature is  provided in R/3 Adapter 5.1.1 HF 3 and higher versions.