Hours after a state judge halted the layoffs of 478 subway station agents, the MTA announced Thursday it will give pink slips to another 1,000 employees — and that could mean dirtier trains.

NYC Transit is taking the biggest hit, with the agency set to lay off 750 employees and reduce the cleaning and maintenance of subway cars. The agency will skimp on removing ugly scratchiti from windows and only clean trains at one end of the route — meaning a car can travel for more than three hours before it is scrubbed.

“This is extremely painful,” said Transit President Thomas Prendergast, who said that trains have been cleaned at both ends of the route since the late 80s.

The new layoffs will save more than $150 million.

The MTA is scrambling to close a $378 million budget gap, and so far has cut roughly $200 million of it.

Meanwhile, a state judge will hear arguments Monday about whether the MTA goofed by issuing pink slips to station agents before holding public hearings on the subject. Workers set to surrender their uniforms Thursday were suddenly told to go back to their booths until the case is decided.

“It’s a relief, but we don’t know what comes next,” said Gordon Clebert, 65, a station agent from Brooklyn.

The MTA expected to save $21 million a year by laying off the station agents, and each day they remain costs the MTA $100,000, Prendergast said. Union leaders expect the legal wrangling to go on for weeks, and will try to lobby for funding to prevent the layoffs in the meantime, officials said.

In other transit news:
- The federal Transportation Security Administration has been screening straphangers’ bags at four stations since March

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- Crime is up slightly in the subways in all categories compared to last year

- Officials pledged to improve the intercoms in subway stations and install them in more entrances

(Julia Borovskaya contributed to this story)