The ink level indicator on the menu is very inaccurate. Also the one in VersaWorks. Wait, as Mike said, till the alarm comes up and printing stops. I never had a problem changing ink in middle of a job. The ink status in Versaworks is helpful to prepare a cartridge for changing. That should be done very quick in middle of a job to prevent from banding at sensitive materials. So the cartridge should be placed unpacked near the back of your machine. Don't forget to push "Resume printing" in Versaworks after change.
But, as you said, the print was faded. Was this solved after changing the cartridge(s)? Have you changed more than one cartridge at once? It's hardly ever that more than one ink runs empty at the same time. Seems, that there is another problem than low ink. I once had an issue, where the indicator of a cartridge didn't work, so the ink tube in the printer went dry. That normally should not happen. And in this case there is no ink left over in the empty cartridge.
Tilo