A long-stalled plan to build hundreds of affordable apartments over the train tracks at Brooklyn’s Atlantic Yards is getting a do-over after two decades of broken promises.

The fresh start means a previous developer will fully skirt millions in ongoing penalties for missing a May deadline to deliver the low-cost housing under the terms of a 2014 legal agreement, angering some local leaders. The monthly fines for each missing apartment were supposed to seed an affordable housing trust fund that could help finance projects elsewhere in the borough.

But a newly approved development team called Brooklyn Ascending Land Co., led by the firms Cirrus Real Estate Partners and LCOR, has agreed to contribute $4.5 million to the fund in the next 30 days, followed by another $7.5 million over two y

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