I presume all your concern is about the CASE ventilation fans, and NOT the fans on the CPU, graphics card or PSU.
FIRST, with the system shut down, open the case. For EACH of those fans, examine carefully its cable of wires.
1. Where does it plug in? Is each on its own separate mobo SYS_FAN header, or are they all going to one central Fan Hub? IF they all connect to one Hub, then that Hub should have one cable that goes to one SYS_FAN header. Which one, in that case?
2. For each fan, how many wires are there in that cable? Or, if you cannot see that, how many HOLES are in the connector on the end? Three or Four? This is important for my point #5 below.
Now to check SYS_FAN header settings in BIOS Setup. When you updated the BIOS it would have used a default group of options which may NOT be the same as you had before, so that could have made changes you did not notice. For each of these headers that actually IS used to plug in a fan, look at these items. Refer to the BIOS Setup Guide downloaded from here
on p. 6-7.
3. Fan Speed Control - should be "Normal" to use default automatic control.
4. Fan Control Use Temperature Input should be Motherboard, not CPU.
5. Fan / Pump Control Mode should be Voltage IF your fans have THREE wires/holes in the connection, OR set to PWM if the fans have FOUR wires / holes. Do not leave this on Auto.
6. Fan / Pump Stop. Do NOT ENable this! Using that feature allows the mobo to shut off the fan when the temperature is lower than a setting you can make here. DISable this feature so that it never stops the fans.
7. Fan / Pump Fail Warning - ENable this so you DO get a warning when the fan is NOT running. As you have seen, this works. When you get the fans to NOT stop, you will get no meaningless warnings.
After you have made all the changes you need for EACH fan header, use the Esc key to back out to the Main Menu (p. 4) then F10 to reach the Exit Menu (p.28). There choose Save and Exit Setup to save your settings and reboot.