I'd like to follow up on this if you don't mind . . .
Are your case fans powered by the mobo?
If no, we should track down why they turned off. If yes, we should track down wtf stopped then started them lol.
Only one of the case fans is connected to a molex, the rest are connected to the motherboard. I didn't happen to check if that one was running or not, sorry. I still have no idea what the problem was, I just left my computer off for a few hours and when I turned it back on, the case fans kept running (they did go from 100% to about 30-40% after 5-10 seconds, the same time they were turning off, so some speed profile was kicking in). I went into the BIOS after this to check and Q-fan was enabled and the chassis fans were displaying RPM speeds when before they just said N/A. I disabled Q-fan for the chassis, booted up, reinstalled Speedfan to adjust manually, and everything is working fine again.