This article explains why the iBGP sessions flaps can be seen after deleting an eBGP session or an RR iBGP session.

After a flap or configuration removal of an eBGP session or an RR iBGP session, other iBGP session can flap, the below log can be seen indicating the flap is caused by the configuration change:

Feb 9 11:27:16 <host> rpd[28368]: bgp_adv_main_update:12142: NOTIFICATION sent to <address> (Internal AS <AS>): code 6 (Cease) subcode 6 (Other Configuration Change), Reason: Configuration change - VPN table advertise

This behavior is expected as per BGP design and is meant to have the routing information updated among the BGP peers.

When a router or switch is configured as either a route reflector (RR) or an AS boundary router (an external BGP peer) and a VPN family (for example, the family inet-vpn unicast statement) is configured, a flap of either the RR IBGP session or the EBGP session causes flaps of all other BGP sessions that are configured with the family inet-vpn unicast statement.

https://www.juniper.net/documentation/en_US/junos12.3/topics/topic-map/bgp-sessions.html