Canon Pro 1000 Inkflow: A Simplified View of How Ink Moves From the Cartridge to the Printhead.
Understanding how the Canon Pro 1000 cartridge delivers its ink to the printhead will help explain some of the mysteries about why topping up ink will still show unchanged levels on the LCD screen.

The ink cartridge is a throw-away piece… at least to the engineers at Canon.
So they kept it as simple as possible to save on manufacturing costs… perfectly understandable. Yes, there’s a chip in the cartridge head, but its prime functions are to identify it with a very specific serial number (every cartridge ever made has its own) and then to designate the cartridge as permitted or not. The cartridge’s chip is not measuring ink use or counting pages. All those functions are handled by the printer’s own internal software located inside the heavy case.
The #1 thing to remember before installing Viewports: Never let the ink cartridge run until it’s completely empty.
If the printer software marks the chip as empty you will never be able to use that cartridge in your printer again, no matter how much ink is put back into it. It’s true that you can re-chip the cartridge (for now) but Canon has decided to start closing off that option. After all they own the copyright on the software used in the functioning of those counterfit chips.
So what triggers the empty status in a Canon Pro-1000 cartridge? How does it know when it’s empty if the cartridge is not measuring how much ink is inside? Let’s look inside:

There is an inner reservoir located inside the printer that the cartridge feeds ink into. This inner tank needs to be fully charged (filled) with ink, so the first setup set of inks that you use when you first install your new printer will be depleted to about half as soon as you set it up. Some of the ink that is used feeds the reservoir and some of it fills the lines and print head.

This is why the ink cartridge is empty when you pull it out of your printer. The cartridge is not actually measuring the amount of ink inside of it. Instead the printer is using the interior reservoir to know when to set the chip to empty.