For quite a while I have been running a Canon iP4200 with my home built constant ink-level CIS. See:
http://www.nifty-stuff.com/forum/viewtopic.php?id=2498 Finally, I have experienced a problem with one color. The cyan started to get a scattered weakness in the Nozzle Check Print. I would run a cleaning cycle and clear it up and proceed with my printing.
Later it became necessary to do a Deep Cleaning to get the cyan to check properly. Still later it required two Deep Cleanings and finally it just stopped printing cyan completely.
I puzzled over this, lifted out the cartridge to see if I could lift the external bottle and get ink to flow, and it did. With the external bottle raised two or three inches, ink would start out the cartridge exit port.
Since wishing didn't make the problem go away, I decided to pull the print head and proceed with testing and cleaning attempts.
Using a thick walled vinyl tube that fit well over the ink inlet port, I tried to pull a vacuum on the cyan port. I use a large 60mL syringe for my vacuum pump. The cyan port would not yield at all. I moved over to the magenta port and with a fairly heavy pull, got magenta ink to come out of the head.
At this time I became worried that my unplugged cartridges might try to dry out, so I retrieved my new backup printhead from storage and installed it in the printer and set it to doing initial cleaning and then set it to doing Printhead Alignment.
Back to the clogged printhead.
With a folded towel paper pad in a shallow dish, I microwaved some water that soaked the pad and came up to a 1/8 inch depth. With the head sitting upright on the paper towel, I pulled the vacuum on the magenta input port and got magenta and eventually water. I returned to the cyan input port and pulled strongly with complete resistance until finally I got a small amount of cyan color out. This was repeated with re-heating of the water from time to time and some long waits until finally, success with the cyan port yielding ink followed by water, with a similar resistance as given by the magenta port.
I visited the other ink input ports and gave them the vacuum treatment until clear water came through. They each offered a similar resistance to that of the magenta. I decided to leave the head with water in the ink chambers for a day, so I sealed it in a ziplock bag with a wet towel paper folded up beside it. Finally I vacuumed out all the water and sealed the head again in the ziplock bag. I certainly believe the head is unclogged, but I have not run it yet.
I want to note something that I observed. Even with the head clean and unclogged, it takes a quite significant vacuum force to pull water into the printhead and out the input port. I know this is not the force caused by the restriction of the ink jet holes, because at one point I had the bottom plate of the printhead disconnected from the top plastic part, far enough to see that the little tubes that couple were separated from the bottom plate with its ink jet hole pattern. In this open condition I still got the strong resistance to a vacuum pulled on the ink input ports. I am guessing that there is some sort of extremely fine filter-like pad in the ink path, and I guess that filter, or whatever, is in the upper part below the metal screen which covers the input port. This may be not so much a filter as it is a functional part of the pumping action of the printhead. I picture the ink being restricted so it can't quickly move back with every pressure shot meant to shoot out a droplet of ink. If anyone has a distinct knowledge of this part of the print head, please let us hear about it.
I decided that I much prefer pulling a vacuum on the ink input ports as I picture anything that is clogging the ink path should not be forced down into the extremely small ink jet openings. Pulling a vaccum on the ink input port seems the logical thing to do, and it is easy to supply incoming water or other liquids by immersing just the bottom of the printhead in the liquid, perhaps aided by a soaked towel or filter paper.