Clannad also recorded “Fairy Queen”, with flute as well though it is very subtle there.
Listen to The Chieftains. They recorded a lot of Carolan (and other harpists) pieces, with flute and whistle. I believe they inherited their love to O’Carolan from Sean O’Riada and Ceoloiri Cualann so listening to them also may help, though I don’t remember if there was a lot of flute there - I haven’t listened to them for long time.
Billy Clifford recorded “Mrs. Edwards” & “David Power” on his “Echoes of Sliabh Luachra, 2010” album.
Deanta has beautiful version of “Eleanor Plunkett”.
Joe Burke played “Blind Mary” on his flute album.
Lunasa played “O’Carolan’s welcome”.
Emer Mayock recorded “Katherine O’More” in fast tempo on her “Merry bits of timber”.
Mike McGoldrick plays “Give me your hand” (though it’s not Carolan but Ruari Dall O’Cathain) on a video on YT.
Cormac Breathnach recorded “Si bheag Si Mhor” on low whistle - there’s a video on YT.
June McCormack & Michael Rooney have a couple of planxties on their albums but I suspect it’s Rooney’s compositions.
I love O’Carolan’s and other harpers’ music and play it a lot but find it quite challenging to play harp music on flute or whistle/ You have to find an approach to make it sound well.
Me and my former band named Rún recorded some pieces by Carolan and Ruari Dall O’Cathain 6 years ago with flute and tinwhistle (listen to them here) - there’s “Eleanor Plunkett” and “Give me your hand” - the former being better, to my mind.
There are definetely more flautists who played Carolan but he doesn’t seem to be very popular with them which I can understand.
Can’t think off-hand of any commercial recordings of O’Carolan tunes on flute (haven’t browsed my CD collection!), but I’ve played several obvious ones since my earliest days as a fluter, probably the Planxty (band) influence! Planxty Irwin, Si Beag Si Mhor, Hewlett, are the most obvious (and of course Tabhair Dom Do Lamh though not by the man…), together with the Swarb version of O’Carolan’s Concerto. Familiar session favourites include Thomas Leixlip the Proud (spurious attribution?), Fanny Power, Lord Inchiquin, Princess Royal (though I know the English version(s) better), Morgan Magan, O’Carolan’s Draught, Henry McDermott-Roe (No.1).
I also often play and have a YT rendition of the questionably attributed Carolan tune Captain O’Kane/The Wounded Hussar - from c 1’ in to the video. It’s luvverly in Gmin - really comfy on the flute!