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Settled ink will effect the color and density of your print output (this effects both color and BW prints, and is a natural trait of all pigment or pigmented inks, paints, etc...). For consistent output from day to day, month to month, etc... regular ink agitation and use of the printer are important steps to maintaining your professional print system and reliable, consistent output.
Settled ink can also cause particles to build up in the dampers faster than normal (requiring they be replaced sooner than the standard 1-3 year guidelines).
Best regards~ Dana