Instead of joining his father and older brother at Birkhall, Harry is said to have remained at Balmoral Castle with the Queen's other children: Prince Andrew, Prince Edward and Princess Anne.
The Duke of Sussex made the trip to Scotland on Thursday – but arrived too late to see his grandmother before she died.
The King was already at the royal castle in the Highlands and William had travelled north earlier on Thursday.
But it now appears there was a "clear divide" on the evening and "two dinners were hosted".
Kate, William, Meghan and Harry at Windsor
PETER NICHOLLS
MailOnline quoted a source saying: "Two dinners were being hosted on the royal estate that night and there was a clear divide.
"One was for the new King and his heir, the other was for the rest of the family."
It also appears that the first the two brothers saw of each other after Queen Elizabeth II's death was on Saturday.
William is said to have texted Harry to arrange a visit to Windsor Castle – and the two were joined by their wives: Kate, Princess of Wales and Meghan, Duchess of Sussex.
It is thought to be the first time since Commonwealth Day in 2020 that the couples have all been in public together.
They could also be reunited for the funeral itself as the brothers are prepared to "put their differences aside".
They were separated by their cousin Peter Phillips at the Duke of Edinburgh's funeral last year.
But William and Harry are "not in the same place" as they were when Prince Philip died and could be ready to brave their differences out of respect for Queen Elizabeth II.
The Sun reports an insider as saying: "We are certainly not in the same place as Philip's funeral when William and Harry didn't walk side by side.
"Things haven't changed but it is not as intense and they can co-exist.
"But the flower visit really doesn't change anything. It is the same situation as at Prince Philip's funeral when William and Harry put their differences aside and supported each other and their families in that moment."
Prince Harry boards a plane in Aberdeen after visiting Balmoral on Thursday
PHIL NOBLE