To C of O, or not C of O

Bought our 2 fam house in Ditmas Park last year knowing the roof would need replacement. The house was built in 1903 and has no C of O, as it predates when C of O’s started. We have refinished the basement (added a full bath) and knocked a wall down in refinishing the main floor.
We just submitted plans to DOB to replace the roof and add two dormers and a full bath on the top floor. They are now insisting that we apply for a C of O, which could cost $10,000 and add many, many months to the project (we are expecting our first child in Nov). One option is to do just do it w/o permits, which we don’t want to do. Another is get a work permit for the interior work, and just do it, and then forget about C of O or apply later, which would subject us to small fines, etc. Any advice? Any problems with not having a C of O down the line, especially if we ever decided to sell (whcih we’re not at this time)? Help???

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