Epson's has a couple of settings related to ANC and auto cleaning. One of those is "auto cleaning times" found in the maintenance menu (hold down pause when powering the printer on).
The current default is 1. When these changes were first made what this basically means is if the printer detects a clog when performing an ANC, it would go ahead and print without cleaning, but display "some nozzles were clogged" in the panel. (Yes, I know. Why would anyone want to go ahead and print if there are clogs).
If you change this number to 2, then if the printer detects missing nozzles, it will go ahead and perform a single cleaning cycle "appropriate for the level of blockage detected". It will then check the nozzles again, if any are missing it will go ahead and print with the warning.
Setting it to 3 means the printer will repeat the clean up to 3 times if necessary. This is the only setting where the printer will not print unless all nozzles are firing. If after 3 tries there are still missing nozzles, you will get a cleaning error, and should intervene with manual checks and cleans.
I'm not sure who decided these are the "appropriate" actions for a printer to take. I don't think anyone wants the printer to go ahead and print if nozzles are missing. I would prefer all 3 choices to have a cleaning error if the nozzles aren't clear ... not print. This would make setting number 2 very useful.
For what it's worth, I have my 7900 set to 3, and I've never seen it trigger a 2nd cleaning cycle so it's been pretty reliable. Using 2 might not be too bad, but like you my new 4900 had some problems early on and required some manual intervention to get things working well. Since then it's been quite good.
Here's a link to read more about the auto cleaning times setting.