Problem
cloned config was not getting applied successfully on the AG device. This was because with the command "clear config secondary" the connection to restapi would be lost as restapi would be turned off when we clear config.
Solution
Similar to what is done for APV where the config of the cloned file is applied doing the same for AG with the command.

Have removed the clear config secondary to resolve the issue

Tested by taking clone config of a device and changing the log settings in the device to 

DEBUG'.

After applying the cloned config the log level changes back to 'INFO' as before