Speaking as a former ship engineer (and designer), the engineering crew is mostly there to operate and monitor the plant. This is done from a computer. Almost everything in a modern engine space is automated or can be operated remotely from the engineering control station (the aforementioned computer). That includes opening and closing valves, starting up and shutting down systems, troubleshooting, and so on.

Unfortunately some times the sensors or actuators break, so an engineer will have to do some manual work. I suspect older engineers are more likely to do this, because they still think their own intuition is better than some algorithm (case in point: see quote in article from the union representative).

As for maintenance, it gets done in port. There are times, however, when things break horribly, and the engineers have to fix it themselves while at sea or find a work-around. With a drone fleet, one way to deal with this may be to have engineering teams on stand-by, ready to helo to a broken drone ship and do repairs.