Have replaced the ink cartridge to a full one. The system is still saying that it is nearly empty. Plus, the light is flashing.

All the ink tanks should be red with no flashing.
The tanks that are flashing or have no red light on , need to be replaced.

While there may be ink in the cartidges, your printer is getting a signal from the cartidge that it's near empty. There is no real workaround for this; you just have to replace the cartridge(s). If you use a LOT of ink, you might consider installing a CIS (continuous ink system) now made for most printers. You will save a lot of money over time.

What you describe is typical.

Canon Bubble Jet orange light flashes

Using the printer's control panel In some circumstances, you may need to replace an ink cartridge before it is empty.
If the ink out light is flashing or is on, replace the empty ink cartridge as described in Replacing an Empty Ink Cartridge.
To replace an ink cartridge before the ink out light flashes or the Status Monitor notifies you that the cartridge is empty, follow the instructions in this section.
Caution: Do not remove the cartridge from the printer until you are ready to replace it with the other one.
Make sure that the printer is on. The power light should be on, but not flashing.
Lower the output tray, then open the printer cover.
Press the ink button. The print head will move to the ink cartridge replacement position, and the power light will begin to flash.
Note: Do not press the ink button over three seconds. Otherwise the printer starts cleaning the print head.

Try unplugging the printer, waiting a few minutes and replugging it back in.

There is a chip on your cartridge that communicates with the printer to estimate how much ink is left in the cartridge. When the chip thinks the cartridge is empty it will refuse to print any more pages no matter how much ink is left in the cartridge. These cartridges are only estimated to print "up to 840 4" x 6" photos, or 80 13" x 19" photos." If it showed half full yesterday and then you put through a large print job it is very likely the cartridge is empty. In any case once the chip thinks it's empty the cartridge needs to be replaced.

If any ink cartridge is empty, you won't be able to print until you replace the empty cartridge. Leave any empty cartridge installed in the device until you have obtained a replacement.

The print heads will clog up in a week or two. So you also won't be able to print until you clean the print heads.

This is a utility to manage your ink. Gives an accurate count of how many ink shots are left in each cartridge. The printer told me I need a new magenta but this program says I have 13% left. It also has separate routines for cleaning the black and color (unfortunately not individual cartridges)
http://www.ssclg.com/epsone.shtml

This is normal.
Printer will warn the ink is getting low. almost empty very nearly empty....

then (in effect) it says if you want to use refilled cartridges you can but it may void printer warranty. Press yellow flashing button for 5 seconds to "release ink detection" (summat like that).

Printer will continue to print but shows the cartridge as empty. Its your responsibility to make sure you do not run out.

It does this separately for each colour - tedious for the pro9000 with 8 colours

1. Make sure the printer is turned on.
2. Make sure the document cover is closed, then closed, then open the scanner.
(Do not open the scanner when the document cover is open).
3. Press and release the ink button. The 'On' and 'Ink' lights flash.
If one of the cartridges is low or empty the printer moves that cartridge to the 'ink out' mark. Go to step 4.
If no cartridges are low or empty the ink cartridge holder moves to the ink replacement position. Go to step 5.
4. Pree the 'ink' button again.
If more than one cartridge is empty or low the next cartridge moves to the 'ink out' mark.
Once the printer identifies all the empty or low ink cartridges the print head moves to the ink cartridge replacement position.
5. Open the cartridge cover, squeeze the tab at the back of the empty cartridge and lift it out.
6. Before you open the new cartridge package shake it four or five times and remove it from the package .
(Don't remove or tear the label on the cartridge otherwise ink will leak out) .
(Don't touch the green chip on the front of the ink cartridge - you could damage the cartridge).
7. Place the new ink cartridge into the cartridge holder and push it down till it clicks into place.
8. Replace any other cartridges that need replacing.
9. Close the ink cartridge cover and press it until it clicks into place.
10. Close the scanner.
11. Press the 'ink' button. The printer starts charging ink and the 'on' light starts flashing . This takes about a minute . When it's finished the 'on' light stops flashing and remains on and the 'ink' light goes out.

You'll see all the above, with helpful pictures, at

this Epson support page

If the firmware update doesn't work, you can reset this error.

Unplug unit. Remove offending cartridge. Plug unit back in, wait until all startup noises have stopped. Open lid and reinstall cartridge. This will solve the fault as long as the sensor is working.

Also, please be aware, you should not have to change a cartridge if it says "Near Empty", only if it says "Ink Empty Magenta".

Also, please make sure none of your other cartridges are empty. I have seen this over and over. Two cartridges empty at the same time, and the person replaces one of them but thinks they actually replaced the other one.

Turn the power off and pull all the cartridges out. Look a the side of the cartridge, you should see a window with a little plastic tab sticking out. This tab should be blocked by a black float inside the cartridge. If you cannot see the float, and the tab is clear with no ink in it and no float tab blocking it, it means the cartridge is empty even if you still see some ink in the bottom.

To be sure plug the machine in without any cartridges. When all the noises have stopped, open the lid and install the cartridges. If you're still getting an error saying either a cartridge is not installed or is empty, then one of your cartridges is empty. Redo the previous paragraph.