I've never found that 'inappropriate' saves (as described above) actually disappear.
What I do find is that odd things can happen. For example if submerged, when you load up you get the tinkling glass from shattered gauges, and I've read that this trasnlates to a slight reduction in Hull Integrity but I can't confrim that. Also things like sunk ships re-appearing etc.
But my saves have never disappeared because of this. Maybe others' have?
Sorry that doesn't help too much but hey-ho...
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