Flores also had a game-tying sac fly in the eighth inning Tuesday and delivered a go-ahead, three-run homer Monday, which helped New York to a 6-3 win.
Flores has had his struggles defensively in 2015, but he is finally turning the corner offensively. He has hit safely in 15 of his last 17 games, while producing four home runs and 13 RBI in that span.
"I truly believe Wilmer's gotten past [his issues]," manager Terry Collins said, per MLB.com. "He realizes there's going to be a day that you're going to make an error. He's got to play through that, and I think he's doing that. We're starting to see a guy who's going to start swinging the bat like we know he can. He's going to put up some offensive numbers that people are going to be pretty impressed by.
"I see a completely different player."
The team has not provided an update on the status of either player, but with the team off on Thursday, there's a chance they could return for Friday's game in Baltimore.
Aviles, who went 0 for 3 with a walk and a strikeout in his team's 4-3 loss on Tuesday, will look to improve his .310 batting average after getting another start under his belt.
"If he comes in and tells me he can play tomorrow, I'll play him. It's kinda on him if he feels like he's ready."
Andrew Romine will get the start at shortstop and bat eighth against the A's on Tuesday.
Segura is currently on the 15-day DL with a broken finger and has been out of action since May 13. Segura is hitting .262 with 12 RBI in 126 at-bats this season and will immediately reclaim his starting role at shortstop.
Santana's return ultimately slides Eduardo Nunez back to the bench on Tuesday.
Harrison will make just his third start in the outfield this season, his second in right. Harrison is hitting .255 with 14 RBI in 161 at-bats this season.
Hardy said that core exercises have helped his back improve, according to MLB.com. He also feels the minor back injury he suffered Monday would have kept him out longer last year.
Hardy recently returned from stint on the disabled list, and has 11 hits over 58 at-bats, including two home runs, in his first 16 games of the season.
Cabrera said he is available to pinch-hit and is hoping to be back in the lineup Friday.