I want to upgrade an app through deployer and apply bundle cluster .Can I update particular app through the UI of deployer and then apply bundle cluster?
No. If you install an app via GUI it will end up in /etc/apps. Apps that you want to deploy to a SHC need to be placed in /etc/shcluster/apps/
Check the "Where to place the configuration bundle on the deployer": http://docs.splunk.com/Documentation/Splunk/7.1.2/DistSearch/PropagateSHCconfigurationchanges
