The Long Island Rail Road’s promise to discount tickets for some commuters inconvenienced by this summer’s planned service disruptions in Penn Station is causing confusion and frustration among riders who purchased their July passes before the offer was made.

On Tuesday, the LIRR announced its plan to discount tickets to and from Atlantic Terminal, Hunterspoint Avenue and some other New York City station by an average of 25 percent during July and August. That’s when an Amtrak track project is forcing the railroad to reduce rush-hour service at Penn.

While LIRR customers can buy the discounted tickets at vending machines and ticket windows, commuters who had already purchased their July monthly pass through the railroad’s Mail & Ride program now have to exchange it if they want to take advantage of the discount.

The LIRR began sending the July tickets out on June 20 — before announcing the discount program.

The railroad has instructed customers to “return your unused Mail & Ride ticket for full credit by simply placing the unused ticket in the return envelope and placing in the Mail & Ride drop box at Penn Station, Atlantic Terminal or Jamaica Station.”

In addition to the hassle of having to return the ticket in person, some commuters have pointed out that they bought their July Mail & Ride ticket using pretaxed dollars through programs like Wageworks.

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Having already used their allotted monthly pretaxed allowance, they worry that they may not be able to take advantage of the benefit again to buy a new ticket.

“I understand they want to incentivize going to alternate stations, but the way they rolled this out was terrible,” said Jason Terry, 36, of Plainview, who typically commutes to Penn but said he’s willing to travel in and out of Hunterspoint Avenue this summer to get the discount. “But at end of the day I’m glad the MTA is giving us a discount.”

The LIRR said Friday that even though some riders have already been mailed their tickets, the railroad typically doesn’t charge accounts until between the 1st and 3rd of the month, so if they exchange their tickets soon, they may still be able to use their pretaxed allowance.

The LIRR Commuter Council earlier this week blamed some of the logistical problems that have come up in the discount offer on the railroad taking too long to roll out its summer plan, and not including input from commuters when putting it together.