Since you have to shut down all other generators when doing a scan (only applies if the individual being scanned is a target of the generators), you might as well as shut down after the scan and pull the pulse out prior to restarting everything back up. Only takes an additional few minutes to do this.
From my experience, if I pull the pulse out while things are running, eventually the system destabilizes and I start getting communication errors.
Having the pulse hanging out the side of the computer will also serve to act as an additional source of interference if you are running plasma.
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