The state legislature reached a tentative agreement to extend New York City’s rent laws, but a cloud of uncertainty still looms over thousands of regulated units affected by a 2-year-old court decision that many hoped would be addressed during the session.

Sources said there were some discussions on how to deal with the fall out from a 2009 Appellate Division of New York’s Supreme Court ruling that owners of Stuyvesant Town/Peter Cooper Village had illegally deregulated units when receiving a tax break known as a J-51. That decision, which affected thousands of apartments beyond those in that sprawling complex, left the door open to reregulating units and reimbursing tenants for overcharges. But since then, neither the courts nor state housing authorities have reached any type of agreement about how to implement the ruling. A Republican senator introduced a bill that would have allowed landlords to pay the taxes while not repaying tenants for overcharges but it failed to gain traction.

“It was a disappointment that they didn’t address the Roberts decision,” said Steven Spinola, president of the Real Estate Board of New York, which represents landlords, referring to the common name of court ruling which stems from the last name of one of the tenants, Amy Roberts, who brought the suit. “”We really think there needs to be a decision by the Legislature since the courts don’t know what to do.”

He added that the Legislature also failed to extend the J-51 program, which extends tax breaks for making building repairs and expires this December. Mr. Spinola hopes legislators will return later this year for a special session, during which the program can be extended. He added that legislators could also address the Roberts decision at that time.

Meanwhile, legislators agreed to grant some small increases in tenant protection as they extended the current rent laws. Presently, landlords can deregulate a unit when the apartment is vacant and rent goes over $2,000 a month or when a family’s income goes above $175,000 and the rent is at least $2,000 a month. Under the deal, the rent limit increases to $2,500 a month in both instances and the family can earn up to $200,000 a year.

“The agreement is much better than it could have been,” said Maggie Russell-Ciardi, executive Director of Tenants & Neighbors, a tenant advocacy organization. “Of course, it wasn’t everything tenants wanted.”

In other developments, the Legislature also agreed to extend the 421-A program which gives developers temporary property tax exemptions to build affordable housing.

“We are obviously pleased with that,” Mr. Spinola said. “It is critical to get building going again.”