PHILADELPHIA — The Mets are crossing their fingers concerning two of the better arms in their Opening Day bullpen.

Drew Smith, who was expected back first Tuesday and then Wednesday, had “a little bit of a setback,” manager Carlos Mendoza said, while Brooks Raley has been diagnosed with a UCL strain and is delaying a decision on surgery.

Smith first: The righty, who has been on the injured list retroactive to April 24 with right shoulder soreness, played catch before Tuesday’s loss and reported “a pinch” on the back of his shoulder.

Smith’s previous issue had been felt on the front of his shoulder.

“We don’t think it’s anything serious,” Mendoza said before the Mets lost, 10-5, to the Phillies at Citizens Bank Park.

Smith did not throw Wednesday and is expected to begin throwing again Thursday.

“We don’t anticipate this being a long setback,” said Mendoza, who added the club did not feel the issue yet required further tests on Smith’s shoulder.

Raley, meanwhile, visited Dr. Keith Meister in Texas on Tuesday and learned he has a UCL strain but one “that is healing,” Mendoza said.

UCL strains often require surgery — a dicey proposition for a lefty who turns 36 next month — and Raley apparently wants to give his throwing elbow a chance to bounce back on its own.

Mendoza said the plan is for Raley to be shut down from throwing for two weeks and then “see where we’re at.”

“I don’t know,” Mendoza said, asked about the optimism that surgery can be avoided. “It’s hard for me to sit here and speculate.”

After shaking up the roster, the Mets shook up the starting lineup, too.

Pete Alonso hit No. 2 for the first time all season, after Brandon Nimmo and ahead of Francisco Lindor.

J.D. Martinez batted cleanup, Mark Vientos fifth and Starling Marte — normally the No. 2 hitter — was bumped to sixth.

“Just trying to get something going,” Mendoza said. “I like Pete’s at-bats as of late. … But I like the versatility of Marte.”

Jeff McNeil, who was down on the dirt for several moments after fouling a pitch off his left knee in the sixth inning, is OK, Mendoza said.

“Got him good, though, but he’s fine,” Mendoza added.

Adrian Houser made his second appearance out of the bullpen and allowed three runs (just one earned) in the final two innings.

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