Having the NMLS # on a 1003 isn't a "compliance" issue at this point, at least the way i understand it. The requirements to have it on a 1003 are coming from Fannie and Freddie as a purchase requirement. If he is the acting LO for the loan and this 1003 is acting as the final application, personally, i wouldn't see a problem with it. I don't necessarily see any reason though for him to retroactively sign the initial application in the departed LO's place; instead, i'd just document the file mentioning the change in LO. Perhaps others will have a different idea.
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I'm fixin' to fix that.