A real problem with the game is that if the boat comes under fire and has to crash dive, the engineer tends to get injured so is unable to repair the systems, so you basically fill up with sea water and croak.
I think systems repair themselves automatically but the engineer can speed up repairs with his special abilities.
This said, he has an ability called repair destroyed systems which can take 5 days plus, never waited around long enough to see if he does actually repair destroyed kit or not
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