By default Auto-Enable Interfaces in Application Settings is set to True and as routers are discovered their interfaces are set to Yes for Enabled whether there is flow on the interfaces or not. There is a case where all interfaces accross all routers (that currenly do not have flow and/or are not Licensed) can be reverted back to No for Enabled. You could run into the following scenario if for some reason RA/NFA is trying to enable an agent (interface) and there is some sort of problem.
Checking the PumpLog####-##-##.log on the RA/NFA Master Console machine may indicate the above problem if you see the following in the log:
18:39:04 4 - DataConverter: Due to errors, disabling all existing interfaces that don't have agents.
Directly above this line there should be an error on the offending router/interface that would need action performed on it to keep the system from automatically disabling all interfaces (that currenly do not have flow and/or are not Licensed).