When the FRB oversaw HMDA, they issued a FAQ (2011) that indicated you should report a loan that is being modified from a construction phase into permanent financing. The CFPB rewrote HMDA and the new rules do not contain this requirement. Instead, the new HMDA rules clearly state to not report modifications. Therefore, the loan you describe would never be reported.
Now, if you knew you were going to do this, there's an argument that should be reporting it as it really isn't a temporary loan followed by a permanent loan. If this is the exception to the rule, then I stand by not reporting it.