Hi Sankar,
sapcpe is the tool which synchronizes the SAP kernel from /sapmnt/exe to /usr/sap/SID/DVEB***/exe
Execution steps are defined in the SAP start profile. You need to check whether it exists in your SAP start profile or not.
Additionally you need to ensure that following soft link exists
1) /usr/sap/SID/SYS/exe/run to /sapmnt/SID/exe
2) /usr/sap/SID/SYS/profile to /sapmnt/SID/profile
Above steps will reduce your manual efforts of copying and synchronizing the SAP kernel.
You will need to update kernel only in /sapmnt/SID/exe only.
Hope this helps.
Regards,
Deepak Kori