I find that the chance of a post-battle CTD increases the longer I've been playing and the more battles I've fought in a session. So I've got in the habit of doing a quicksave before every battle, and of quitting and restarting EB completely after 2-3 long battles.
When a CTD does occur, I reload from the quicksave, type 'auto_win attacker' (or defender, as appropriate) into the console on the pre-battle screen, and just auto-resolve it. Yes, you'll typically take more casualties, but it's better than 30-60 minutes of your life
IMO the advice never to save before a battle and never to use a quicksave is less than helpful. The post-battle CTDs have all the hallmarks of a memory leak growing to the point where the process cannot allocate more memory when it's trying to switch modes from "battle" from "campaign". Saving or not saving should have little or no impact on this. I diagnose this sort of stuff in my day job, so I've been meaning to hook up the process to some tools and figure out what's happening. The problem is playing to the point where I can reliably trigger a post-battle CTD. Repros are always the hardest!
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