By definition, automatic systems are the default go-to: They kick in automatically. Fitted systems remotely operated may or may not be used immediately - it's a command decision.
However, wether we are talking of automatic systems or fitted systems, many such systems are disabled during refits, just as many of the hatches and watertight doors are in a state where they cannot be operated. Refits are always very dangerous times onboard a warship, with many potential and actual incidents, accidents ... and disasters just waiting to happen.
The good news, if that is possible, is that being in refit, her airplanes and marines would have been landed and any tank not being worked on would likely have been topped up (I know, counter-intuitive, but a filled AVGAS or Diesel tank is less dangerous than an empty or near empty one, where the fumes are highly explosive).
