Just had this conversation with my repair guru after replacing the head on my second-hand 9900 that I've had and used for ten years.
I've had that problem once and a while and the only easy way to deal with it is to run some jobs. In my experience, if only a nozzle or two in a head or two are not showing as clean, it's not a big deal. I had that issue with one color after I started using the printer and could never get it totally clean. After the professional cleaning and running several prints through the works, the channel came back 100%.
It's debris (lint, pet hair, etc) that the head catches and accumulates and no matter how many cleaning cycles, it remains. His advise for when I print canvas or other linty/dusty papers is to vacuum around the paper intake afterwards so that it doesn't get further down toward the head. He also showed me how to get to the head with minimal disassembly to gently clean the crud around the head occasionally advised that once cleaned, dry it. Same with the other subsystems that do the cleaning. YRMV and you are on your own if you do this!
In my ten years, I've had him clean my printer one time several years ago and it worked great until this year when all indications pointed to the head finally giving up the ghost. It's now replaced and running just like new!