hey, i don't see any temperature readings.
Adding water with a difference in temperature of more than 2 degrees, can make your fish act weird, like gasping and hanging at the surface.
Did you refill with the same temp water as the original tankwater?
A clogged filter can indeed hurt your bacteria, but would usually result in an ammonia spike.
I had my share of sleepless nights, when things were troublesome or risky for my fish.
You're a good fishkeeper, if i see how you can worry about your fishes well being!
Respect for that!