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UCD9090 Microcontroller Configuration Programming

Other Parts Discussed in Thread: UCD9090

I have a UCD9090 in circuit and running that I want to programmatically do a partial reconfigure from a microcontroller. Is the best method to write specific PMbus commands from the uC or to rewrite the data flash using a data flash script or other?. If I use PMbus command and  store_default_all, are there commands I should avoid with this method? If writes using "E2 and E3" commands are used and the data flash is not first erased what is the result?