DIAGNOSIS The printer estimates ink levels based on page count and nozzle usage, not by physically measuring the ink left. It's notoriously inaccurate, especially if you've done a lot of print head cleanings.
FIX You can reset the ink level indicator, but it's a manual process. When the message says 'Ink Empty' for a color, you can continue printing for a while. To reset the monitor, the printer needs to detect a new cartridge. Take the cartridge it says is empty out, inspect it (if there's actually ink in the sponge window), and then re-insert it firmly. Sometimes it will recognize it as 'new' and reset the counter. If not, you may need to temporarily put a piece of tape over the cartridge's sensor window—this is a well-known workaround, but do your research on the exact method for your cartridge model.
IF THAT DIDN'T WORK The printer's internal counter might just be stuck. A full power cycle can help. Turn the printer off with the side switch, unplug it, wait 60 seconds, plug it back in, and turn it on. This won't reset the level, but it can clear the persistent warning message temporarily.
HEADS UP Printing with an 'empty' warning won't harm the printer. It will eventually stop when the ink is truly, physically depleted. The warning is more of a reminder to have a spare cartridge on hand rather than an exact gauge.