Will My Feral cat use litter box again?

So we have this feral cat boy who has been coming around for a while now, id say half wild half domesticated, and hes just barely 1, he comes and goes everyday, he pulls the door open every-night to let us know hes there, anyways months back maybe 5 or 6 we got him using a separate litter box that we bought, and there was success but, the other cat which is a girl isn't territorial but like to be a punk a few times she had ambushed him while he is going, and ever since he doesn't use it just meows at the door when he has to go, is there anyway i can get him comfortable to use it again?