Decided for Side by Side migration
Why? This requires far more work including reconfiguration of things that can't be migrated (like client settings), client redeployment, and lots or orchestration of things like remote site systems.
Also we have Intune integrated with old SCCM server and it is comanaged. If i transfer the clients to new server with new site code. Will this affect the intune enrolled devices.
Yes, of course it will. I don't think that we have a supported path or any defined steps for performing a migration when a site is cloud attached so I honestly don't know all of the implications here other than the current site is definitely connected to your MEM/Intune instance.