Many last-minute tax filers may be in for an unpleasant surprise as they race to beat the federal filing deadline that hits at midnight Wednesday. For those who received federal subsidies that helped them buy health coverage in 2014, the federal government might want a chunk of that money back.

An estimated 45,000 Louisiana residents will either get a reduced refund or actually have to pay. On the plus side, roughly 41,000 can expect to get larger-than-expected refunds.

The trick is whether they underestimated or overestimated their income when enrolling for health coverage under the Affordable Care Act, also referred to as Obamacare. In many cases, enrollees in the federal marketplace received a government subsidy that was based on their estimated income to help pay for the insurance coverage.

Before completing her return Tuesday, Eleanor Faust, a Baton Rouge home nursing aide, wasn’t concerned about the Affordable Care Act’s impact on her taxes.

“It’s not complicated at all. My insurer, they mail you a tax form, and all I have to do is present it to (Volunteer Income Tax Assistance at) Catholic Charities, where I’m having my taxes done,” Faust said.

But after her return was completed, Faust learned she had to give up part of her tax refund to repay a portion of her subsidy.

Under the Affordable Care Act, enrollees can qualify for a premium tax credit. The credit is based on their estimated income. The credit can be taken as an advance payment, which goes directly to their insurer. Close to 90 percent of the lower- to moderate-income people who enrolled in the federal marketplace in Louisiana received a federal subsidy.

Catholic Charities VITA Site Coordinator Marlene Martinez said the Affordable Care Act enrollees’ tax returns share a common problem: underestimated income.

That’s what the VITA site at Catholic Charities of the Diocese of Baton Rouge is seeing while helping about 1,300 people do their taxes this tax season. The local VITA program, overseen by Capital Area United Way, will help 5,300 prepare returns.

Faust underestimated her income because it was based on a job she had when she enrolled under the health care law. Faust left that position for another with better pay. She also worked a second job for a while. The result was Faust’s actual income in 2014 was higher, putting her in a position of having to pay back part of the subsidy that was based on the lower income estimate at the time she enrolled. Luckily, that repayment ate up just a part of her tax refund, so she didn’t actually have to come up with cash.

The Kaiser Family Foundation estimates that half of the subsidy-eligible households nationwide will owe some repayment of their subsidy because of underestimating their income, while 45 percent will receive a bigger refund because they overestimated their income. Early returns processed by H&R Block and Jackson Hewitt showed similar results. The Louisiana numbers are based on those percentages.

The average repayment nationally is $794, while the average refund is $773, according to Kaiser. However, for most low-income filers, the subsidy repayments will only reduce their refunds rather than require them to pay additional taxes, according to a report by the Tax Policy Center, a joint project of The Urban Institute and Brookings Institution.

“The confusion comes when they have changes in their household or in their income, and they don’t contact the marketplace within 30 days to adjust their payment,” said Veronica Coleman, manager for H&R Block’s New Orleans East office.

Martinez said that lots of times, federal marketplace workers don’t remind enrollees to call if their income or family size changes.

Steve Everly, Jackson Hewitt district manager in Baton Rouge, said repayment amounts can be substantial. Instead of getting a refund, some people are having to pay the IRS for the first time in years.

“We’re seeing people that are having to pay as much as $2,500 back to,” Everly said.

Brian Burton, who heads Louisiana’s largest navigator group set up to advise enrollees, said repayments are limited for lower-income filers.

For families whose income is between 100 percent and 200 percent of the federal poverty level, the maximum repayment is $600. For families between 200 percent and 300 percent of poverty level, the maximum is $1,500.

“I think the most important take from this is that it is proportionate,” Burton said, “meaning consumers should either make the changes in the front end during the year when they know their income is changing or have to refund it on the back end and return the oversubsidized amount.”

Everly said Jackson Hewitt is seeing another issue related to the Affordable Care Act.

Some lower-income clients are mistakenly paying the ACA penalty — $95 per adult or 1 percent of income, whichever is higher, Everly said.

Penalties are only owed by people who don’t have insurance.

Meanwhile, H&R Block and other tax preparers are warning Affordable Care Act enrollees to file a federal return or an extension Wednesday. Those who don’t could actually miss out on financial help for coverage in the future.

Each year, about 7.5 million U.S. taxpayers who should file a federal return don’t, according to H&R Block. The tax preparer didn’t have current figures for Louisiana, but in 2011, 22,000 of the state’s residents who didn’t file returns passed up a total of $21.4 million in potential refunds.

Follow Ted Griggs on Twitter, @tedgriggsbr.