[XenonSurf]

For the long time I played TWoS I never did the Scapa Flow mission. From other players, there should be no problems with this one because it's a scripted mission contrary as to when you enter ports by your own decision.
The TWoS docs - and other posts about slipping into ports are clear: The traffic AI and the escort AI (the logic they use to follow and combat you) can get messed-up if you engage and sink ships in ports, the reason is that most 'traffic nodes' coded to spawn traffic in the game are technically placed near ports and do NOT apply in such locations (about 40 km around port).

Translated into clear and crisp language this means:
If you go into ports you will meet no resistance once you are in (except minefields and port canons obviously), so it's not interesting and more of a tonnage cheat to do it; all the traffic in your campaign can get messed-up (but maybe not).
Unfortunately there is no sign when this happens. Only sign could be that you will never make any encounters of convoys anymore where you should.

But by following the rules about how to save the game, which is: save everytime in a different slot and everytime you enter bunker, you will have no problem to reload an old save and restart from there - and not doing the Scapa Flow mission to avoid corruptions.
If you stay away from enemy ports you will never run in this sort of problems - or you must get prepared to reload a past save.


BTW, I think this problem also applies to SH3 and SH4.