Solution
The channels that referring about (SET.Base.RefFaultCon, SET.Base.RefFaultSet0, SET.Base.RefFaultSet1, SET.Base.Ref0 and SET.Base.Ref1) are used to set the relays on the SET-2010 for connecting the reference signals on the front I/O connector to the fault bus on the Rear I/O. For example, you might set those channels to connect J2REF4 to Fault Bus A.

All relays are default open on power-up unless the default state is changed in the topology file. If another startup state is desired, the topology file can be edited to add new topologies that will put certain relays in a closed state when the card boots up.