my money is on ink dropout.
your test pattern printing 100%? your ink cartridges full? (or at least >1 on your levels. heck, forget what it registers... just pull the cart out, and turn it over. if a noticeable amount of ink stirs from one end of the bag to the other, then you're >1)
post pics of test print and enhanced/enlarged photos of the error in your prints to confirm. you should see distinct lines in the print if only half the head is printing, or no lines at all but noticeable lack of c/m/y/k if it is an entire head misfiring.
printer is fed via a light siphon-pressure of ink. when the flow stops, so does certain dots of color in your prints. can either be from air bubbles in your ink lines, cracked head manifolds, bad o-rings in dampers, bad dampers in general, bad seals between damper and ink lines, bad ink pump not refreshing the siphon (same can happen when capping station doesn't make a proper seat on the printhead), etc. also, sometimes a cart will register 1, but really be empty. easier to start there and narrow-down your diagnosis... if I'm correct with your issue.
noted: that encoder strip issues usually restricts the misplaced color droplets to the area below contamination. if your entire print is missing color across the entire y-axis, unless your entire encoder strip has ink smeared across it, then the issue is most likely ink-supply.