Before the ex-Hampshire batsman announced his decision to retire from 50-over cricket - and therefore Twenty20 internationals too, under the terms of his England and Wales Cricket Board contract - Flower tried on several occasions to persuade him to carry on.
With the decision made, irrevocably it seems, Flower is well aware and frank about the loss to his England ODI team.
"When Kevin told me he wanted to retire from one-day cricket I must have had three or four subsequent meetings with him where I tried to dissuade him from doing so," Flower said.
"I think it's really sad he won't be playing all three forms of the game. He's in incredible form - technically, he's excellent."
There was an ongoing plan in place to accommodate rest periods for the South Africa-born batsman, to help prevent burn-out from playing all three international formats.
"He can rest - it's not as if KP can't ever rest - we do rest him, and if you look back at various series that's what we've done," said Flower.
"He's also had significant chunks out with injury; it's not that he doesn't get a chance to rest."
Pietersen, 31, made it clear he would have much preferred to continue playing Twenty20 cricket. But he will now be restricted to Tests.
"All the players and the players' representatives signed up to that," added Flower.
"You can't choose between one of the limited-overs formats - it's there in black and white.
"Kevin is very clear that he doesn't want to play one-day cricket any more, so that makes him unavailable for Twenty20 cricket. That's an ECB policy."
Flower believes there is good sense behind that stipulation too, to protect the status of one-day cricket, and because England are still trying to win their first World Cup in that format - after 10 failures to date, since 1975.
"The reason for that policy is that 50-over cricket is an integral part of ECB strategy," he said.
"England have never won a 50-over World Cup, and we are very hungry to do so.
"The board is also very concerned about setting the right precedent. If you set a precedent whereby players can pick and choose between the limited-over forms, they are worried about five or six players doing a similar thing.
"This would degrade limited-overs cricket. This policy is in place for a good reason, and Kevin and his representatives were aware of that.
"I hope that after he's retired he doesn't regret that, but that's the decision that's been taken."