Root, the England captain, appeared to suggest Moeen had unilaterally decided to leave the tour with two Tests of the series remaining.
"Moeen has chosen to go home," Root said at the time. "It's obviously been a very tricky tour for him. As mentioned at the start, if players feel like they need to get out of the bubble, then that's been an option. With Moeen it wasn't more asking if he wanted to stay, it was a decision he had chosen."
In truth, Moeen's break from the tour had been arranged by the selectors several weeks previously and was consistent with the team management's policy of giving all their all-format players a break from the bio-bubble at some stage on the trip. Ben Stokes, Jos Buttler, Sam Curran, Jofra Archer, Jonny Bairstow and Mark Wood have all had similar breaks.
Root's comments sparked something of a backlash across the media. Although some defended Moeen, others latched onto the words to express their dissatisfaction on the incorrect assumption that he had left the tour on something of a whim, having been recalled to the Test team just a week previously.
Realising that his choice of words had been somewhat clumsy, Root sought out Moeen when the team returned to the hotel after the game on Tuesday. He explained that he had not expressed himself clearly and reiterated Moeen's value to the team. He also clarified his support for the rotation policy and his appreciation of the need for players to balance their family lives alongside their professional commitments.
Moeen is understood to have accepted the apology and departs the tour on good terms with the team, its captain and coaches. He returns to India at the end of the month as part of England's T20I squad and retains hopes of being picked up in the IPL auction.
Now Silverwood, the England head coach, has made the apology public and confirmed the decision to rest Moeen during the tour was made by the team management and not by the player himself. He also confirmed they had asked Moeen on the third day of the second Test whether he would consider staying with the Test squad, but says that ultimately the team management decided it was "the right decision for him to go home".
"First of all, we're sorry," Silverwood said. "The impression we gave yesterday was Moeen's been treated different to other people. He isn't. I can guarantee you that.
"The decision for him to go home was ours as it was with Buttler, Sam, Bairstow and Wood, to be honest. So, we're happy to own that decision.
"It was a unique situation with Moeen. He had spent so long in isolation getting Covid out in Sri Lanka and he had just broken back into the team. The question was posed to him [over whether he would like to stay on tour], do you know what I mean?
"We try and work as closely as we can with players to make sure they get the best opportunities as well as looking after them. So it was asked. But ultimately, we felt it was the right decision for him to go home."
While the incident has led to some speculation that Moeen's Test career could be over, Silverwood insisted he was a "very big part" of England's plans for the Ashes, which is scheduled to be played at the end of this year.
"We're trying to build a big group of players we can use moving forward," Silverwood said. "The planning and building for the Ashes started a long time ago and we're continuing to build that group of players. At any given point, anybody can play. Moeen is a very big part of that."
Although the incident has underlined the difficulty of touring in the time of Covid, Silverwood maintains England's rest and rotation policy is the responsible way of ensuring players - and support staff - are able to juggle their careers and personal lives. He also said that Moeen had accepted the clarification from Root and knew the team management had "his best interests at heart".
"I think it's the life we're living at the moment," he said. "We have to prioritise looking after our players and we're doing the best we can. Being locked in a bubble for long periods of time is difficult, especially with people who have families at home. We have to be very respectful that people need to see families. And equally families need to see them as well.
"We touched base with Mo last night - as did Joe - and he was fine. He understands we've got his best interests at heart and we're trying to look after him just like all the other players in the strange times we're in."
George Dobell is a senior correspondent at ESPNcricinfo