Interesting. I alt-tab to windows (10) extensively due to video capture (I have OBS stop recording on ctrl-alt-S, but SH4 ignores the alt and interprets it as emergency surface, as I found, luckily not in combat), and I haven't seen any problems yet in-game (and all the problems with replay are known issues w/o tabbing).
I had about three CTDs so far as well (fingers crossed).
Only other problem I tend to run in is CO2 not resetting on surfacing, where I have to save/reload.
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