Are you getting any warnings with that motherboard about missing fans/ramping fans up? I have the same motherboard but in an intel chassis with 2 delta fans in the front and 2 original heatsinks. But when ever I disconnect a fan or replace that fan with a different fan the motherboard will freak out and ramp up the front and psu fans to the max. I want to watercool this chassis by placing 2 radiators on the delta fans in the front but it will ramp those up if the cpu fans are missing so that isnt really gonna work.
As I understand it, if you change the configuration of the system fans, you'll need to run through the FRUSDR setup utility again. This is one of the last steps of 'flashing a bios', so get the latest intel BIOS package for that mobo, extract and copy to a USB stick, boot the system to the UEFI shell and run the FRUSDR tool.
Also note that if you open the chassis while the system is running, a chassis intrusion SEL (system event) will be tripped which will drive the system fans at max rpm until that SEL is cleared. So if that occurred, clear the SEL either through the BIOS setup menu, or BMC web console, or via IPMI.