SEPTA's loss of one-third of its rail cars last summer created so many delays that the transit agency put on hiatus a refund policy for riders whose trains were late.

The rail cars eventually came back, but the refund didn't. On Tuesday, SEPTA reported that  the refunds are gone for good.

The service guarantee allowed passengers to request a full refund on Regional Rail tickets if a train was more than 15 minutes late to its final destination. The policy applied to the two city subway lines, the Norristown High Speed Line, and the two suburban trolley lines, but was most used on Regional Rail.

SEPTA would provide a refund within six to eight weeks, but there were conditions. The policy applied only to weekday trains. A refund request form had to be filed within five days of the late train. If the train was late due to an act of God, extreme weather, or circumstances out of SEPTA's control, such as problems with track owned by Amtrak, the guarantee didn't apply.

The exemptions made the program more nuisance than benefit, said Kim Heinle, SEPTA's assistant general manager for customer service. SEPTA received hundreds of claims a month, he said, and about half were rejected.

"We were creating a situation where we were making our customers even more frustrated," he said.

Regional Rail's 13 lines move about 65,000 riders a day throughout Philadelphia and its suburbs, to as far as Delaware and Trenton. Late train refunds cost SEPTA about $22,000 in fiscal year 2016, officials said.

The refunds were axed amid a plague of lateness that SEPTA can't seem to shake. When 120 Silverliner V rail cars had to be pulled from service in July because of flawed load-bearing beams, on-time service plummeted to the low 60 percent range. By November, when a strike paralyzed city transit, Regional Rail had a 79 percent on-time rate. That number improved slightly to 81 percent in December.

January's numbers weren't finalized Tuesday but were comparable to December's, officials said. SEPTA's stated goal is a reliability rate of 90 percent or better.

"Clearly, with the service-guarantee program in place, SEPTA would have been paying out a lot on that," said Matt Mitchell, vice president of the Delaware Valley Association of Rail Passengers.

The agency introduced a new schedule on Dec. 11 that did not improve reliability much, Mitchell said, and on Sunday SEPTA introduced another big schedule change. Adding to the confusion was SEPTA's decision not to print updated schedule pamphlets for stations.

Killing the service guarantee wasn't a money-saving move, SEPTA said. Such refunds are increasingly rare, and SEPTA officials have long contemplated ending theirs. Long Island Railroad, Boston's Massachusetts Bay Transit Authority, and the Chicago Transit Authority all offer no refunds for lateness, according to those agencies.

Instead, SEPTA wants to use its smart fare-card system, the Key, to reward loyal riders, Heinle said.

"We knew we needed to introduce something different," Heinle said, "redefine the customer relationship, base it on patronage and loyalty."

How hasn't been decided, but Heinle mentioned incentive programs and partnering with businesses to create discounts.

SEPTA unveiled the Key card incrementally for city transit, subways, buses, and trolleys last year. Regional Rail users should expect a similar rollout this year, said Rich Burnfield, SEPTA's deputy general manager. Meanwhile, SEPTA Key should be fully available for all transit users this spring, he said.

Reasons for lateness include the introduction of the Positive Train Control braking system, conflicts on rail shared with Amtrak, the age of equipment, and a lack of personnel. That staffing shortage, in particular, has contributed to train cancellations. And, because it takes so long to train new engineers, the disruption isn't likely to end soon, said Richard Dixon, of the Brotherhood of Locomotive Engineers and Trainmen.

Getting rid of the service guarantee was a mistake, Mitchell said, when there is so much about SEPTA service in flux.

"There weren't a lot of people who were taking advantage of it," he said. "What it did do was to let off some of the pressure for some of the people who were particularly frustrated with the performance of their train. At least they're getting a refund. That's something that mollifies them."