tjncooke: Yes, I shake ink bottles and carts pretty hard, then let them sit for a few minutes before filling carts or using the printer.
anachronon: All pigment ink settles when left sitting still, even Epson ink. It's less obvious visually when you have settled color inks, since there are SO many colors, but with Piezography ink it can be very obvious since B&W prints are made of density, which is easier to see a change in. Epson instructs customers to shake carts before use, and use within 6 mo- this saves them from recommending customers shake ink to keep it in suspension, and 6 mo time period saves them from issues due to older or settled ink- they'll just tell you to get new ink. We have learned pigment ink settles, but it can be used safely for about two years after it's made (and longer than 6mo after installing into the printer)- as long as carts are regularly agitated and the printer is regularly used to maintain consistent results.
Cartridge recognition is controlled by the cartridge chips and printer's chip sensors, so if the Epson carts stopped being recognized after removing + shaking, then I'm not sure what caused this... strange.
LarryB: Yes, you may get a tiny air bubble when carts are removed, though that amount of air shouldn't be enough to effect/restrict flow like large sections of air will. Maybe it would be best to remove + shake carts with the printer OFF, so there's no suction or pressure on the ink lines (?)
Best regards and happy printing to all~ Dana