When you end patrol and reach bunker, always save in a separate slot first if you intend to reload the game, do not use bunker autosaves. You can however continue from the bunker immediately if you want (but I would also save in a separate slot just for security). And you should know that when starting a career or chapter you must *always* save / reload to avoid these quirks and CTDs. In TWoS this is written onscreen now.
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