Steps to reproduce:

1. Create template with host_prototype. Add 3 custom interfaces - SNMPv2 to template host_prototype. 
   
2. Create Autoregistration action with operation - Link to templates.
3. Start server and agent.
4. Wait till host with host prototype is created.
5. Turn off server and agent. 
6. Unlink template from created host.
7. Update template - remove all SNMPv2 interfaces from host_prototype and add one SNMPv3.
   
8. Change hostmetadata in etc/zabbix_agentd.conf
9. Start server and agent.
10. Wait till tempalte is linking to host again.

Result:
In template there is one SNMPv3 interface. 
IN created host_prototype there is two SNMPv2 and one SNMPv3 interfaces.

Expected:
Created host_prototype updated and has only one SNMPv3 interface.