I like to imagine the HoF went into his/her mission alongside Oghren and Nathaniel (in fact, I headcanoned that for my Warden-Commander Tabris), since they are the only Wardens from Awakening that matter in the Keep (even the Orlesian Warden-Commander got the Shrug of God). By that point Velana possibly was searching for Serani in the Deep Roads and Sigrun... either died or was with the HoF.
As for the other Fereldan Wardens, The Last Flight novel says that by 9:41 Dragon the Wardens of Vigil's Keep were still active, and there was even a new Warden-Commander in Ferelden, meaning the HoF may have "disappeared" (aka. began the search for the Cure) around 9:40/41 Dragon. As for the Orlesian Warden, his/her epilogue says that s/he will be eventually recalled to Weisshaupt when rumors of another Blight began to grow in the Anderfels... that makes a lot of sense with what Morrigan says in the epilogue of Inquisition (the silence from Weisshaupt, hinting at something really wrong happening there, that Morrigan hints to regardless if you ally or exile the Southern Wardens).
As for Clarel's letter... well, the new Warden-Commander of Ferelden in the novels seems a little bit incompetent (had problems with a few Sylvans...). So, maybe Clarel thought she can replace him or whatever.
And the bulk of the Fereldan Wardens, is possibly they got caught in Clarel's "tragic mistake" (seeing the incompetency of the new Warden-Commander, is very likely), and were at Adamant alongside the Orlesian Wardens.