Virtually all of my saves are made submerged since I mostly play in 1944-45 and being on the surface often ends badly. Cannot recall when last I had any file corruption issue or loss of a saved game so saving while submerged in itself is not a problem.
The advice regarding proximity to ports (as opposed to just land), the presence of enemy forces or aircraft is well taken and I would add never save when using any TC > x1.
In my experience just saving while submerged is fine provided you stick to the above caveats.
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