CLMOR-F to LOMR-F

We prepared a CLOMR-F for a building with a foundation. Endangered species held it up for months, but eventually the NFIP approved the plan. Construction has ended and we filed for the LOMR-F. It was flagged as illegal construction of a basement within a SFHA and sent to the Regional Office for review. The Compliance Officer is reviewing it, but his first comment was along the lines of: Why wouldn't they have issued the LOMR-F after the approved CLOMR-F?

We included All documentation within the filing of the LOMR-F including the CLOMR-F.
Flood maps are the same.
Fill was a little lower than design (LAG = 11.8 design, 11.4 constructed, BFE = 11 per map and I have not looked at the transect in 2 years to see that result) but the fill was still above the mapped BFE.
This is within a stillwater AE, coastal flooding, over a mile from the ocean.
The Compliance Officer's manager confirmed that 10-01 is still applicable and has not been revised in the past few years.

Anybody have insight?