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Seeing your mention of the previous NPE being applied sent me googling today, it seems that it is a message that can generally be ignored. It is supposed to be a correction for non orthogonality between the two axis and it will only be re calculated on a three star alignment.
I use my AZEQ6 (The Orion version but it is quicker to type AZEQ6) with ASCOM and manually home it before use with ASCOM, but my sons goto dob pops that message up pretty much every alignment.
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