It wasn’t a facade. The developer building a massive housing complex on the site of the former Long Island College Hospital filed plans for two towers on Wednesday, dashing some residents’ hopes that its earlier threats to build a high-rise over the Cobble Hill Historic District were just a bluff to push residents into supporting a rezoning. But, just as promised, the plans show builder Fortis Property Group is planning a 15-story residential structure on a low-rise brownstone stretch of Henry Street, confirming locals’ worst fears that their brownstone-lined nabe will soon be overshadowed by tall buildings.