Hi Kapil,
so the folder structure as shown in BI Launchpad is indeed as defined within the CMS security for a user.. As you mention you upgraded your BI4.0 into BI4.1, i'd suggest to check the security settings on the top level folder (CMC -> Folders -> Manage -> Top Level Security)..
some changes have been made to the default security settings on top level between 4.0 and 4.1 and could cause that users do not have the right to see the top level folder.. without the view rights on Top Level folder, any subfolder will not be visible as well.
regards
Merlijn