Can I fight the New York City Department of Buildings?

The NYC DOB has had my request for renovations to my home in Brooklyn that we purchased 2+ years ago. We have DOB emails admitting to "lost" folders for over a year, and when I got involved by calling the commissioner(s), the folder was miraculously found. Now that I voiced the lack of support from the DOB, my project seems to be stonewalled. I have an architect, engineer and expediters working on this to no avail - and they simply blame the DOB. As the owner - paying for all of this, real estate taxes, mortgage and utilities, it doesn't look like they will work with us. What recourse do we have? I feel like I'm being discriminated as I see similar projects moving in our neighborhood.