Debugged it further and found that agent sends delayed subscription to control-node. Due to missing subscription, control-node doesn’t re-originate the route.

Routing instance config rxed:
2016-02-26 15:52:53.298 AgentXmppMessage: Received xmpp message from: 172.16.180.8 Port 5269 Size: 770 Packet: <?xml version="1.0"?> <iq type="set" <email address hidden>" to="default-global-system-config:csol2-node11/config"> <config> <update> <node type="routing-instance"> <name>default-domain:obs-sc:net-right:service-9f0454e8-e5e0-4dc1-91f5-41662750b95d-default-domain_obs-sc_obs-in-net1</name> <routing-instance-has-pnf>false</routing-instance-has-pnf> </node> <link> <node type="virtual-network"> <name>default-domain:obs-sc:net-right</name> </node> <node type="routing-instance"> <name>default-domain:obs-sc:net-right:service-9f0454e8-e5e0-4dc1-91f5-41662750b95d-default-domain_obs-sc_obs-in-net1</name> </node> <metadata type="virtual-network-routing-instance" /> </link> </update> </config> </iq> $ controller/src/vnsw/agent/controller/controller_init.cc 839
2016-02-26 15:52:53.383 AgentXmppMessage: Received xmpp message from: 172.16.180.8 Port 5269 Size: 357 Packet: <?xml version="1.0"?> <iq type="set" <email address hidden>" to="default-global-system-config:csol2-node11/config"> <config> <update> <node type="routing-instance"> <name>default-domain:obs-sc:net-right:service-9f0454e8-e5e0-4dc1-91f5-41662750b95d-default-domain_obs-sc_obs-in-net1</name> </node> </update> </config> </iq> $ controller/src/vnsw/agent/controller/controller_init.cc 839
2016-02-26 15:52:53.436 AgentXmppMessage: Received xmpp message from: 172.16.180.8 Port 5269 Size: 835 Packet: <?xml version="1.0"?> <iq type="set" <email address hidden>" to="default-global-system-config:csol2-node11/config"> <config> <update> <node type="routing-instance"> <name>default-domain:obs-sc:net-left:service-9f0454e8-e5e0-4dc1-91f5-41662750b95d-default-domain_obs-sc_obs-in-net1</name> <service-chain-information> <routing-instance>default-domain:obs-sc:net-right:net-right</routing-instance> <prefix>83.1.1.0/24</prefix> <prefix>84.1.1.0/24</prefix> <service-chain-address>81.1.1.6</service-chain-address> <service-instance>default-domain:obs-sc:obs-in-net1</service-instance> <source-routing-instance>default-domain:obs-sc:net-left:net-left</source-routing-instance> </service-chain-information> <static-route-entries /> </node> </update> </config> </iq> $ controller/src/vnsw/agent/controller/controller_init.cc 839
2016-02-26 15:52:53.436 AgentXmppMessage: Received xmpp message from: 172.16.180.8 Port 5269 Size: 807 Packet: <?xml version="1.0"?> <iq type="set" <email address hidden>" to="default-global-system-config:csol2-node11/config"> <config> <update> <node type="routing-instance"> <name>default-domain:obs-sc:net-right:service-9f0454e8-e5e0-4dc1-91f5-41662750b95d-default-domain_obs-sc_obs-in-net1</name> <service-chain-information> <routing-instance>default-domain:obs-sc:net-left:net-left</routing-instance> <prefix>81.1.1.0/24</prefix> <prefix>82.1.1.0/24</prefix> <service-chain-address>83.1.1.6</service-chain-address> <service-instance>default-domain:obs-sc:obs-in-net1</service-instance> <source-routing-instance>default-domain:obs-sc:net-right:net-right</source-routing-instance> </service-chain-information> </node> </update> </config> </iq> $ controller/src/vnsw/agent/controller/controller_init.cc 839

Subscription sent after ~3 mins

2016-02-26 15:55:53.179 XmppTxStream: Sent xmpp message to: 172.16.180.8 Port 5269 Size: 386 Packet: <?xml version="1.0"?> <iq type="set" from="csol2-node11" <email address hidden>/bgp-peer" id="subscribe632"> <pubsub xmlns="http://jabber.org/protocol/pubsub"> <subscribe node="default-domain:obs-sc:net-right:service-9f0454e8-e5e0-4dc1-91f5-41662750b95d-default-domain_obs-sc_obs-in-net1"> <options> <instance-id>6</instance-id> </options> </subscribe> </pubsub> </iq> $ controller/src/xmpp/xmpp_connection.cc 209
2016-02-26 15:55:53.179 XmppTxStream: Sent xmpp message to: 172.16.180.5 Port 5269 Size: 386 Packet: <?xml version="1.0"?> <iq type="set" from="csol2-node11" <email address hidden>/bgp-peer" id="subscribe633"> <pubsub xmlns="http://jabber.org/protocol/pubsub"> <subscribe node="default-domain:obs-sc:net-right:service-9f0454e8-e5e0-4dc1-91f5-41662750b95d-default-domain_obs-sc_obs-in-net1"> <options> <instance-id>6</instance-id> </options> </subscribe> </pubsub> </iq> $ controller/src/xmpp/xmpp_connection.cc 209

I have taken gcore of grouter-agent when it has VRF struck in deleted state.