The Kolben chronicles: more likely it was her reports for the Brooklyn Paper, not the Daily News, that alarmed Ratner
The answer: likely none committed while writing for the Daily News.
A review of Kolben's Daily News work shows exactly two articles, both co-bylines, concerning Atlantic Yards. A 6/24/05 article was headlined HOMES UP FOR GRABS Ruling ramps up anxiety in city. A 7/6/05 article was headlined A VISION SOARS IN B'KLYN. Yeas, nays over plan for Nets.
While the former article was--like much other initial coverage--somewhat alarmist about the effects of the Supreme Court's Kelo v. New London decision, the latter was essentially balanced.
(Update: I'm told Kolben also contributed to the Daily News as a non-staff stringer, though those articles are not accessible via a database search. Here's one, and another.)
Was it the past work?
So, perhaps Forest City Ratner had gotten wind of tougher coverage in the works at the Daily News.
More likely, however, they were peeved by Kolben's record at the Brooklyn Paper, where she wrote skeptical articles like the 7/17/04 SILENT PARTNERS, about an attempt to find out who was buying the New Jersey Nets; the 7/3/04 RATNER’S MONEY PIT, a sympathetic account of a critical report on alleged tax benefits from Atlantic Yards; and the 6/26/04 Watchdog calls for arena ‘ULURP’, about the importance of putting the project through the city's land use review procedures.