The issue was with the SQL Server Native Client driver in root servers not supporting TLS1.2.
The ODBC connectivity from root servers to remote DB servers failed due to this.
Upgraded the SQL Server Native Client and the issue was resolved.
Tested the ODBC connectivity from root servers to remote DB servers successfully and all is good.
In my original post, I mentioned reconfiguring the ODBC to 64-bit ODBC-driver in the root servers. This is not good, as it only solves one issue, you will remain to have replication as another issue, thus please don’t do this. Upgrade the SQL Native Client driver in the root servers instead seamless and no reconfiguration of ODBC is required.
The remote DB is ok, as it has the driver that supports TLS1.2, thus no action required at remote DB servers in most cases unless you using a much older MSSQL version.
Hope this update will be helpful to those embarking on the TLS setting to disable weaker TLS1.0 and TLS1.1