Just a question: Why are there creature entries present in savegames? When I open a savegame in Enchanted Editor, there are entries for apparently every vanilla creature. This in itself is not problematic, but I had a problem where I removed a mod which changed some of these creatures and apparently on a few of them, the model path did not get replaced by the one that was used with the new mod configuration. This led to some errors and I would never have discovered this if I had not opened the savegame in enchanted editor and seen the wrong model path. I could manually replace it with the correct one, but even repairing the save with Wrye Mash did not do this on its own. Any idea why this is the case? Apparently everything else gets more or less immediately adjusted if the mod configuration is changed, but in this case it did not happen. Could it be because after deleting said mod there was not other mod which changed the creatures? But why then did the standard model path not get restored? I mean I managed to solve the problem but I'd like to know why this happened.

The game keeps track of how many, and what type, of enemies you kill.

If I understand your problem correctly, it may have been caused by enemies that have already spawned, so they are active in the save file.
But Wrye Mash has a "Remove Spawned Creatures" feature for save files.