I was having such a frustrating time with my base last night. I was out on a reconnaissance mission where I FINALLY found a wreck that had the grapple arm for the Prawn suit. I get back to my base, which has a hull integrity of +25 or so, and the thing is flooded. I was confused, so I started putting in bulkheads and adding hull reinforcement. I'd close bulkhead doors, I'd get the message about draining procedure initiated, and half my base would be clear, but half of it remained completely submerged. I went out and harvested lithium so I could put hull reinforcement everywhere, up past 80+ hull integrity. I swam around the entire outside with the repair tool looking for leaks. Nothing.
So, it turns out that leaks don't show on the outside of your base; you can only see them from inside. And if you have any leaks, your base will flood until they're repaired. So apparently something came along and damaged my scanner room, which developed leaks that I could not find, and it submerged everything. Took me nearly an hour to figure this out. On the plus side, not only do I have a Prawn suit with a grapple arm now, I also have a base that I can expand without worrying about hull integrity ever again.