Try not to stress over the bees, I'm sure they'll do fine. Sometimes there is fighting even if there were not a queen in one of the hives combined. From what you say, you see a couple hundred dead or so, maybe more, and that is minor compared to the boost in population you now have after the combine.
We are in the time of year where it's best not to be messing with the hives. If they are light on stores then maybe feed in a non invasive way, but they'd have to be very light for me to mess with them now. Feeding syrup just adds to the moisture in the hive, if you feel they need more feed, try feeding dry sugar over a sheet of newspaper trimmed so that it has space around the edges for bees to get thru on the top of the top bars of the top box with an empty box and lid on top of that. But I'd do that only if the hive seemed very light in stores, and it sounds like yours do have stores already.
20+ years, raise my own queens, feed when needed, I treat but have not perfected varroa management yet.