My interpretation was that Clyde had been wrestling with an ambivalent state of mind, struggling with a desire to return while also fearing separation from Yuu. In the moment he began to disappear and Yuu shows him that desperation as a response, its likely he realizes how much he doesn't want to leave him behind more than he wants to go back, and also how much Yuu doesn't want him to go either. It serves to mentally and spiritually ground him there henceforth. I also saw it as him making a sacrifice in that moment, to prevent Yuu from becoming injured (since he was about to take a nasty fall down the stairs from phasing through his body), and that instance of instinct driven by his desire to protect likely overrided the spiriting away that was about to happen, kind of like when a ghost has such strong desires that they can't move on even in death. Sort of sealed his fate, as it were
I think his resolved feelings of wanting to be together with Sugimori(the uke) made his body stable
I just didn't understand, at one point he actually began to disappear? But that's it? Then he just didn't?