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My hive reversed itself? (PA-European)

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My hive reversed itself? (PA-European)

I'm sure it'll be obvious from the post but I'm new to bee keeping. This is my first year and I started with one hive. I just recently moved to a farming community that is all Amish (I am not) and I'm having trouble finding any local mentors. I've been reading alot of books and so far everything has gone pretty much according to plan. I started my hive late because I had trouble finding a nuc. I set my bees up the last week of April. My property borders an apple orchard but I missed the orchard bloom by 1 week. I moved the nuc into a 10 frame large Langstroth after 1 day but they still swarmed after 3 weeks. I found the new queen and marked her and then left them alone for a month. Mid-June they were doing great and I added a second box. Two weeks later I opened the box to do a mite check and immediately I could tell something was up. Up to that point I hadn't been stung and they were extremely mellow but this time I opened the box and they were instantly pissed. I got stung about 12 times in a matter of minutes. I took the hint and left them alone. Two weeks later I checked again and did a mite wash and all was well but my marked queen was definitely gone. I couldn't find a new queen but did see eggs less than 3 days old so I let it be. In early August both boxes were 80% full so I put a queen excluder on top and added a honey super. At that time I still couldn't find a queen but the hive had great brood patterns and was obviously thriving so I didn't look to hard. Here is the weird part. Today I went to open the honey super and see how full the frames were. The honey super had 8 frames all full of capped brood. I did not see any eggs, but did see some larva about 3-5 days old. I looked closely at every frame, no queen. Some of capped brood was emerging and I actually watched them chew out and emerge. (Very cool). Then I opened the middle box and it's all capped honey, no eggs no brood. The bottom box had a mix of everything. So what is going on? The only way in is through the bottom? How do I have brood on both sides of the queen excluder? And why is the middle box all honey? Is it possible the queen is really small and passing through the excluder? Could I have somehow trapped her in there when I added the honey super?

One last question, previously, there were very few mites (I used sticky traps to check) but I visibility saw a few today. Not alot but, enough to treat. Any danger treating this late?

Any help is appreciated!

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