That is a bad idea, he will toast the miner,your first guess however makes a lot of sense, the second fan status is showing 0 rpm on the miner status page, however this should not stop him from being able to upgrade to a different firmware ( someone corrects me if I am wrong, I never tried it but i don't see why it shouldn't happened)
Anyway OP, you should first confirm that both fans are working just fine before trying anything else, if this turns out to be another issue when I will try to guide you on how to troubleshoot the miner, but nothing will make any sense as long as you are not getting the 2 fans to show up, a simple troubleshoot would be swapping the fan cables the goes to the control board, see if Fan2 then shows 0 and another Fan shows any rpm reading, if that happens then you have faulty fan for sure.