Re: Got stung made mistakes how to recover
if i understand correctly, you now have two hives each with a deep and two full supers.
the yellow jackets and other bees were probably attracted to your feeder, especially if you added anything with a scent to the syrup.
the bees boiling out of the second hive must have been trapped in the top because the bee escape got clogged up with bees.
i guess it depends on what you were wanting to do with the honey. i'm not sure about indiana, but i would think that a deep and two mediums full of stores would be enough for overwintering.
i would rather leave them that honey than have them store syrup, it's a lot healthier for them.
i would guess that if the colonies are strong, things will settle down in a day or two.
good luck, and welcome to the forum.
disclaimer: novice beekeeper here who knows just enough to be dangerous