Unfortunately with SH3 it's a bad idea to save anywhere near anything at all, and it's a worse idea to save submerged. Sometimes it can be alright, but a lot of people have reported corrupted saves, saves not loading and other problems.
Many years ago I saved a game just before entering my home base. When I reloaded it all the ships in the harbor had lost their waypoints and were crashing into everything in sight. It was pretty funny and I did manage to end the patrol alright. When I loaded it again they were still crashing, but I got out safely and the rest of the game was alright after that.
Do it if you have to, but don't be surprised if that's the end of it.
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“Never do anything you can't take back.”
—Rocky Russo
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