If I understand correctly, then no need to remove "double links" because you loose functionality in either the pendant or somewhere else where the state of the machine is needed.
Just connect the whb.halui.machine.is-on with the signal in your basic.hal that is connected to the pin halui.machine.is-on. For example, if the signal is named MySignal then:
net MySignal whb.halui.machine.is-on
