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We replaced a units mainboard which changed the serial number of the unit. We are now needing to enroll into the Apple DEP program. Any ideas how to do this?

You need to be a trained Apple tech within Apple or authorized service center (and only a few get access), it is highly controlled! To reprogram the systems firmware to the users serial number Apple DEP is a very different program: Corporate-owned deployments made simple It allows large companies or schools a means to manage their Apple gear.