Help! Problems with frames, queen cups, and premature brood

Hello,

I need help. I’ve had my flow hive since April. Everything was going well. They were drawing out comb naturally, and brood pattern was great on frames. I’ve recently started to notice some varroa in my bottom tray, but know that is normal. I am going to test for them once my counter comes in. We’ve had heavy rain, and I noticed yesterday immature pupae thrown in the front of the hive. I decided to do an inspection and the brood pattern for a lot of the frames was very unorganized, there are several long, things that look like queen cups. I decided to pull one of the failing frames and put a new frame in, thinking maybe it’s a fungus or chalk brood. Is my queen failing? I need help on diagnosis.