I have bunch clients pointing to deployment server A, I need to make those clients to connect to deployment server B and not any more to DS A. Is there some way I achieve this through Splunk and not edit the configuration on server manually?
It depends. If you follow best practices and put your .conf files in apps which you push to clients then it should be possible. Just update the deploymentclient app and wait for the clients to install it.
OTOH, if your only deploymentclient.conf file is in $SPLUNK_HOME/etc/system/local then you may be stuck doing manual configuration changes because apps cannot override the settings in etc/system/local.
Another option is to create a scripted input that edits $SPLUNK_HOME/etc/system/local/deploymentclient.conf. Push the script to the appropriate clients then delete the app once the task is complete.