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NMIS includes a feature which will disable collecting of interfaces which are down for a period of time, by default, this is 30 days, this is because if down for 1 month, it is likely the interface is not being used anymore.  This feature can be disabled by setting the value in the Config.nmis for global_nocollect_interface_down_days to a very high number, like 5000 or more.  Or the interface can be set in Node Config to always collect.

This feature is based in the ifLastChange MIB for each interface. By definition, ifLastChange is "The value of sysUpTime at the time the interface entered its current operational state. If the current state was entered prior to the last re-initialization of the local network management subsystem, then this object contains a zero value.". Some Fortigate devices have been identified as not updating the ifLastChange when ifOperStatus is changed. That will set the interfaces with operational status down as no collect after sysUpTime days is greater than global_nocollect_interface_down_days (30 days by default). In this case, setting global_nocollect_interface_down_days to a really high value is recommended to disable the feature, to prevent the interfaces not being collecting were they should be.