Canon Pixma Pro 100 Nozzle check revealing missing colors

The Hat

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It was definitely the cartridge.

Filling for over a year is not usual, but if you don’t replace the cart when it’s showing low then ink flow issues tend to appear later, so next time, don’t wait change it immediately..

To bring the cart back to good condition purge with Windex, dry and refill..
 

PeterBJ

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The problem with the cartridge is caused by the ink in the sponge being replaced with air when the reservoir is empty and you continue printing. The problem doesn't start after the cartridge being emptied once but maybe after 5-6 refills. I think topping up before the reservoir is empty as suggested by @The Hat is a good idea. For this topping up i think topfill is the best method.

The cartridge with the air filled sponge is most likely still useable after a reconditioning. You can flush the cartridge with water until the sponge is clean and after that flush the cartridge with pharmacist's conditioning fluid. After the treatment with the conditioning fluid the cartridge should be dried. I think that ghwellsjr's paper towel method works very well. I have had the best results with the cartridges still being slightly moist, not bone dry. A properly refilled CLI-8 cartridge in good condition weighs 27 grams +/- a few tenths of a gram. I think the CLI-42 cartridges are physically identical to the CLI-8 cartridges so the same weight should apply. Weighing the refilled cartridge is a good quality control of your refill and a health check of the cartridge.

You can read more about sponge problems in this thread and in this very long but also very interesting thread. Here are some videos explaining the posts by mikling. I have also tried to do a form of hybrid vacuum/top refill to solve the sponge problem see this post. The method is similar to the one in the first video here "Vacuum Prime".

Also notice in the image in my post that the sponges in the two magenta cartridges are not perfectly white but has got some magenta spots. I think that is a symptom of the "killer fungus" that ruined some printheads years ago. I always inspect the ink outlet before refilling a cartridge. If the cartridge is not flushed and dried I drip a few drops of pharmacist's conditioning or cleaning fluid into the ink outlet. If the outlet does not become white but appears spotty I think that cartridge should not be refilled. But that is another story.
 
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