According to the log, one of the hashboard doesn't detect and the two hashboard is fine all ASIC chips are detected.

I think your title is misleading? The chip you are talking about it supposed to be "a hashing board" am I right?

Anyway, Have you tried to downgrade the firmware? I heard that November firmware can solve this issue, but the problem I don't have any source where to download it.
Try to flash it with this firmware Antminer-S9-all-201711171757-autofreq-user-Update2UBI-NF.tar.gz
Then check if it solves your issue if not please post the new "kernel logs"

The final solution that comes to my mind is to reflash it using "PICKIT 3". If the one of the hashboard is broken you can revive it by using "PICKIT 3" and you can fully erase the program then reflash it with working hex file from other hashboard.

Check this guide from here repair a T9 + after a bad firmware (lost chain)This guide may work well too in S9.