Chicago Public Schools is making a surprising announcement that could cost the district millions of dollars.

In a letter being sent to principals today, CPS CEO Barbara Byrd-Bennett told schools they would again be held harmless for students who didn’t show up this year.

The district changed the way it funds schools last year. Instead of funding positions and programs from downtown, schools are now given about $5,000 per student on average, under a formula called “student-based budgeting.”

Last year, because the system was new, the district allowed schools that didn’t meet enrollment targets to keep the money allocated to them anyway.

In a call with reporters about layoffs in June, Byrd-Bennett insisted that would not happen again.

“No no no, that was last year, remember, and I preached that over and over that it was a one-time hold harmless,” she said.

But now, she’s changing her mind. In the letter to principals, Byrd-Bennett wrote that CPS plans to use “student-based budgeting transition contingency funds and anticipated surplus from Tax-Increment-Financing funds” to make sure schools get money based off their projections, not actual enrollment.

The letter also said any school that got more students on the first day would get additional money.

CPS used to take an official enrollment count on the 20th day of school and now takes both a 10th day and a 20th day count to calculate any potential budget adjustments. The 20th day count will take place on Monday.

District spokesman Bill McCaffrey did not say how many schools came in below and how many came in above their initial enrollment projection. He did not say how much it will cost to essentially pay twice for students or pay for students who are no longer in the district.

McCaffrey also would not say if overall enrollment is up or down. Enrollment in CPS had been steadily declining for the last decade. Last year, the school system lost about 3,000 students, dropping from 403,461 to 400,545.

Becky Vevea is a producer and reporter for WBEZ. Follow her @WBEZeducation.