This KB explains the usage, support and example of Isis-instance configuration.

Most of the time isis-instance configuration is confused with the isis protocol running under a routing-instance.

user@lab#show routing-instances ABC
instance-type virtual-router;
protocols {
    isis {
        interface xe-0/0/46.0;
        interface lo0.0 {
            passive;
        }
    }
}
interface xe-0/0/0.0;
interface lo0.0;

and then when you try to configure isis-instance, you get a commit error

user@lab# set protocols isis-instance ABC interface xe-0/0/0.0 

user@lab# commit check 
[edit protocols isis-instance ABC]
'interface xe-0/0/0.0'
IS-IS: interface is not in this instance
error: configuration check-out failed

This is because the isis-instance config is available at the global level, the device is trying to find xe-0/0/46  in the global routing table, but since the interface is already part of routing-instance ABC, the commit fails

• The isis-instance configuration and isis protocol running under routing-instance are 2 completely different configuration type and are independent of each other. isis-instance is configured on global routing table.
• The isis-instance configuration statement is not supported at the [edit routing-instances routing-instance-name protocols] hierarchy level. 
• You can configure and run multiple independent IGP instances of IS-IS simultaneously on a router. These instances are associated with the default routing instance, and they install routes in the default routing table.Each IS-IS instance can also export the routes installed in the routing table by other IS-IS instances using the standard Junos OS routing policy configuration. By default, the routes installed by the different IS-IS instances have the same route preference.
• While configuring ISIS under routing-instance will create separate routing table for each routing-instance.