Flores’s initial performance as the Nationals’ backup catcher this months only raised more questions about his surgically repaired right shoulder, which suffered a labrum tear and forced him to miss most of 2009 and all of 2010. In his past two games, he answered them.

In the Nationals win over the Mets on Sunday, Flores answered them. He threw out both runners who attempted to steal second, killing a rally by throwing out Willie Harris and ending the fifth inning by throwing out Jose Reyes, who had stolen 32 bases in 38 attempts and is only one of the most electric players in baseball.

Before Wednesday, Flores hadn’t thrown out any runners in seven chances this season, an unsettling development since he missed most of 2009 and all of 2010 after surgery repaired a torn labrum. After Sunday, he’s thrown out the last three runners who tried to steal against him.

“I can feel confident I can throw the ball to the bases well,” Flores said. “When I’m not used to playing every day, it’s different, because you cannot feel that rhythm.”

Flores has played once every three days, taking over Ivan Rodriguez’s role as Wilson Ramos’s backup. (Rodriguez called Manager Davey Johnson this afternoon, a sign that he may be raring to leave Miami, where he has received physical therapy for the last week.)

“It’s been a good situation for him playing behind Ramos,” Johnson said. “Sometimes it’s hard when you’ve gone through something as severe as he had to trust it and feel you can push it a little bit and make it stronger. The tendency sometimes is when it’s not hurting to say, ‘I better not push it.’ ”

The adjustment to less playing time has been difficult for Flores, who in May 2009, before a foul ball gave him a small fracture in the right shoulder, had become the Nationals’ regular catcher. Asked about how he feels about his place in the organization, Flores thought for a moment.

“It’s tough to answer,” Flores said. “I’m happy to be back in the big leagues. It’s been a difficult two years. I feel happy for Wilson, he’s having a great season. I can’t control the decisions. I can just control what I do on the field, and that’s what I’m worried about.”

Lately, what he’s done on the field has been promising. Flores felt comfortable with arm strength even last weekend in Los Angeles, when the Dodgers stole three bases in three chances off him. He explained that Nationals pitchers did not hold runners close and gave him virtually no chance to throw out the runners; Johnson concurred.

Still, his throws yesterday were clearly stronger. The reason is not completely arm strength. Bench coach Pat Corrales, who oversees Flores when he throws before games, said he has improved his form, too.

Flores has a tendency to drop down to a three-quarter motion, but he has started throwing over the top. He also quickened his footwork, which led to a quicker release. Johnson said Flores’s throws yesterday reached second base in less than two seconds, which is considered elite. After a long recovery, Flores’s throws yesterday provided a strong sign.

“It’s starting to come with work and dedication,” Corrales said. “He’s going to be fine.”