First, there is an after credits scene where we see One eyed Owl spit Yoshimura out and then release its kajuka kagune for that big reveal that she was his daughter as pointed out in the question.
After that, we do not see him again in Root A. Season 3 continues the story a few years later and closely follows the mangas overarching story. We do find out some of what happened to him, which simply was that he became a new Kagune farm like Rize was. This is best shown by a new Ghoul introduced in RE:, named Owl as well for having Yoshimura's Kagune. For those who haven't seen season 3, spoilers, but this new Owl's true identity was never hidden and it is
Seidou Takizawa, the side character eaten by Noro at the end of Season 2, and Akira's friend and classmate.
A few others were also given his Kagune as well, and we do see one of them who escaped but is unnamed and hidden in Season 3. Code-name Floppy by CCG and a cannibal ghoul killer, though most people already know or have a good guess who it is.
Yoshimura is however, never seen in season 3. As for his fate in the now ended manga, and spoilers for season 4 when/if it comes out,
he is never seen again. There is one picture of him suspended in fluid in one of those human sized vats commonly used for experimentation, but he is at best unconscious, possibly dead around the Rose extermination which Season 3 ended with. Truly never seen or even mentioned again after that and presumed dead.