You will need to replace the air pressure system (APS). It is a small mechanism clipped under the ink supply station, fairly easy to replace. The replacement procedure is in the service manual which can be downloaded from MANUAL.
The part you need can be ordered here: http://www.lpscomputer.com/p-2507-c6090-60084-designjet-5000-5500-aps-air-pressure-system.aspx
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