UPDATED: 11/4/2011 1:26 a.m.

CHICAGO (CBS) — The Emanuel administration and the Chicago Teachers Union are calling a ceasefire in their continuing skirmishes over a longer school day for the Chicago Public Schools.

But as WBBM Newsradio Political Editor Craig Dellimore reports, differences remain.

The union had been seeking an injunction to block the longer school day from taking effect this year for the 13 schools that agreed to the plan. Those schools were given financial incentives, including a teacher raise, in exchange for extending the day.

LISTEN: WBBM Newsradio Political Editor Craig Dellimore reports

Teachers Union president Karen Lewis still feels Mayor Emanuel and schools chief executive officer Jean-Claude Brizard violated the union’s contract by allowing some schools to break ranks with the union and extend the day on their own.

Still, the union is abandoning that legal maneuver, which will allow those schools to have the longer day.

“We need to have it clear that this was illegal. All right? That’s what we want clear,” Lewis said. “But we don’t want to have to spend a lot of time in court doing that.”

In exchange, the city will not expand the longer day to other schools this year, CBS 2 Chief Correspondent Jay Levine reports.

“For me, it’s a big hope that we’re now in a new place, a new phase of our relationship,” Brizard said.

The relationship got a boost Thursday when the two had an all day meeting behind closed doors in Mayor Rahm Emanuel’s office.

“We’re now going have our energy where it belongs — in the classroom and not the courtroom,” Emanuel said.

Now, the two sides will negotiate a longer school day for the entire school system, starting in the fall of 2012.

Emanuel and Brizard have made lengthening the school day a top priority since they took office. The union balked at the plan without negotiations. Thus, school officials asked individual schools to break ranks and agree to the longer school day on their own.

As a reward for lengthening their school days, each school was promised an extra $150,000 in funding from the Chicago Public Schools. Teachers at the schools are receiving $1,250 bonuses and the 2 percent raises.

Thirteen schools agreed to the offer.

Schools like Skinner North used the additional 90 minutes for recess, writing workshops, technology classes and other enrichment programs. Officials say Skinner and the other schools with longer days will now be studied to see what works best.

With the mayor’s proposed 7 hour 30 minute day, Chicago would go from the shortest to the longest school day in the state.