What you are seeing is different than a normal clog, and in fact I don't believe is a clog. The issue of 9900 class printers dropping an entire channel during a print run is common. Mine does it, especially after a PK to MK or MK to PK switch. No clog I know of can cause a total stoppage of just one channel cleanly. This is unfortunately something in the electronics, or pressure supply. There is no way this could be a "clog" as the printer was working perfectly before it drops the entire channel. Traditional clogs show up as deflections or a missing series of lines from the nozzle check, not the entire pattern. If you have some time do a Google search on this issue, you will find a lot of well written blogs and web articles describing this dropping of an entire channel behavior on the 9900 family.
I recently was forced to have a head change, and during the change, Epson also replaced the dampers. Since the change, I have not seen this problem, (last 6 months). Usage for me is the same. I strongly believe this 100% channel drop is due to a pressure drop or simple electronic fluke where something in the head or ink delivery system has a momentary failure. In the past, the only way I can get the channel back, is to run a CL2 level cleaning from the Service mode menu. I realize this is a cleaning, however this level of cleaning does release and re pressurize the dampers. Basically resetting the in delivery system.
Back to your question, I don't think that the auto detect will help. You sadly have to watch the printer and see if all of a sudden one of the prints looks off, i.e. you no longer are using one of the ink's. In my case it was orange 55% of the time and Yellow and Light black the rest. The Light black issue when it happened was hardest to see in the prints.
In a large job series, I just make it point of stopping and running a nozzle check to see that all the channels are firing. Since the work was done on my machine, I have not had this issue, but it's way too much of a cost for me to see a 36 x 72 canvas come out missing a channel.
Paul