It may or may not necessarily be a message.
If, when you mouse over the 'red bar', the damage value, or whatever you want to call it, is equal to 1 (1.00), then that component is gone, it's destroyed. Whether you always get a message, I dunno, but 1 means totally kaput.
You were good enough to state your fuel situation, so I know that wasn't the issue, but, FWIW, you can have batteries that are damaged and that will never recharge back to 100%. You can use them, but their capacitance has been reduced for the rest of the patrol. If you ever see this, watch your recharge, 'cuz you can burn through your fuel all too quickly trying to recharge batteries that never are fully charged. You have to manually decouple the recharger in this case.
Also, while I'm thinking about it, if you load a save where the boat was submerged, you might have serious issues on getting back to a true surfaced condition. It's a glitch - you'll be at 16 feet depth, but the CO2 keeps going up and the crew can suffocate on a sunny day. Just something to be aware of - avoid saving while underwater, if you can. I just reload again if I have this, seems to work, but the best thing is to save only on the surface with no contacts and no land nearby.
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