The coach has made it clear Pietersen must be amenable to "face-to-face" and "man-to-man" talks to clear the air with him and Test captain Andrew Strauss if he is to find a way back into the England fold.
Pietersen was dropped for the Lord's Test against his native country after failing to divulge the content of texts he sent to opposing players during the draw at Headingley.
Asked whether England can reclaim the world number one Test position they lost to South Africa this summer without his runs, he said: "Without a doubt. English cricket has a great history - and it has a great future.
"It is bigger than any one player. You will always move on from anyone - whether it be a captain, a coach or a player."
Pietersen was also, predictably, left out of England's final 15 for next month's defence of their ICC World Twenty20 crown.
If the 32-year-old is to rediscover any favour with his employers, it seems he is sure to have to not only come clean about his texts - which reportedly contained derogatory references to Strauss - but convince them again of his ongoing goodwill, following a summer of unedifying and distracting contract wrangles.
Pietersen was replaced at Lord's by Jonny Bairstow, who responded with 95 and then 54 in a losing cause.
Fast bowler Steven Finn also converted the fine form he has previously shown most often with a white ball for his country into a fearsome second-innings spell, and an eight-wicket match haul. For those and other reasons, Flower - as he has proven many times before - will not be frightened of taking a difficult decision.
"I think the most important thing is that we do the right thing for England cricket," he said. "That's how we will make our decision.
"Jonny Bairstow handled the situation - and the skill, timing and courage he showed was outstanding. (James) Taylor has handled himself calmly as well.
"We'll make our decisions based on what is best for the England side - and not be scared to do so."