The issue with fatigue subs is that, generally speaking, the AI tries not to be too aggressive at shifting around your lineup. When your cleanup hitter is sitting out, it will naturally take the lineup with the replacement swapped into that spot. Now, usually if they are a worse hitter like a Counsell or Sanders, it should swap them down in the lineup. But if there's something preventing that (do you have a force lineup spot on any of those other guys lower down?), it might not find a suitable swap. When it subs in for defense it doesn't try to rebuild your lineup from scratch necessarily, since most teams tend to stick with their normal lineup but just take a few small tweaks, when someone sits.
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