England team director believes Kevin Pietersen will return for the tour of South Africa but is uncertain whether Andrew Flintoff will play for the national team again.
Pietersen was forced out of the Ashes series after the second Test with an Achilles injury and the 29-year-old's recovery subsequently suffered a setback after developing an infection in the scar tissue.
The Hampshire player had initially been included in the NatWest series of one-day internationals and Twenty20 clashes with Australia but now both he and Flower are looking to the tour of South Africa in November.
Flower told Sky Sports News: "He is still struggling a little with that wound in his Achilles.
"I spoke to him yesterday but I think we are confident in saying he will be back for South Africa."
Pietersen was forced to look on as England reclaimed the Ashes without him and Flower admits he had to be philosophical about his absence.
"Sometimes you never what is good or bad luck," he added.
"Kevin and I spoke about that and he is using this as an opportunity to get some time away from the game.
"It is enforced time away and he didn't want it and we didn't want it, but since it's there and there is nothing anyone can do about it, I think he has got to make the most of it.
"I think that is what he is doing.
"He is spending time with his family and his wife and getting a break from the international game."
Flintoff made his exit from five-day cricket after the triumphant fifth Test at The Oval and immediately underwent knee surgery.
Although the all-rounder intends to return for one-day games, his future has been questioned and Flower is unsure whether Flintoff will ever play for England again.
"I don't know," he said. "I really hope he does. If he can come back and play one-day international and Twenty20 cricket for us and bat at six or seven and bowl like he can bowl, that will make us a force to be reckoned with in one-day cricket.
"Whether he will or not I don't know, I just hope he does."