Now, according to a report on Britain's mirror.co.uk website, Flower has told the board it's "me or KP".
It's a claim that Flower has already denied.
But first hand observations would suggest the pair aren't exactly close.
After England lost the first Ashes Test in Brisbane, they journeyed to the Red Centre for a sightseeing trip to Uluru and a two-day tour match in Alice Springs.
Pietersen was rested from the drawn game against a Chairman's XI but with temperatures in the low 40s he did occasionally run out the drinks and appeared to be making some attempt to be part of the team.
However as the squad waited at Alice Springs Airport on Sunday December 1 for a delayed flight to Adelaide, Pietersen was cornered by Flower for a heart-to-heart chat.
England were short of a No.3 following Jonathan Trott's return home with a stress-related illness and Pietersen was one of several batsmen who could have slotted into the key role.
Flower's body language suggested he was asking the South Africa-born superstar if he was up for the job.
The meeting could well have been a flashpoint in the coach's attempts to manage the divisive Pietersen.
A series of questionable dismissals and bizarre periods fielding on the boundary rope, seemingly banished from the inner circle, would suggest the chat wasn't a great success.
The 104-Test veteran says he's keen to play on and help England regain the Ashes in 2015.
England's need to have a batsman of KP's class in the side is still strong but the desire, at least from the coach's viewpoint, may be wavering.