Yeah, I also overwrite all the time and never have bad saves as a result.
I really think RR is right about the superstition thing.
One thing that I know for a certainty is bad for the game though is alt+tabbing, probably also with certain popups (like steam or antivirus) trying to show on top compounding the problem. This screws up the games estimation of your depth in relation to sensors somehow. Easily observable is the condition in which CO2 will not drop after surfacing. The opposite can also happen. I.E. I routinely have targets become alerted to my presence when they shouldn't if I have alt+tabbed. For example, a couple of days ago I was working with a convoy attack test mission and had them detect me while submerged at silent running from over 6,000 yards away.
In general, these days I always save just before I move to intercept and look out for the specific condition above.
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