Only one chain is appearing in Miner Status on Antminer S9
Is there a possibility one of your power-supplies have gone bad? You can further debug this by obtaining the "Kernel log" found on the "System" tab. I would also try re-seating the cables, and test each hashboard individually (power them one at a time to determine if they are still OK -- make sure to shutdown/unplug your miner before performing any work!)

If you can provide that file, more information should be available.