Clay Buchholz has had a hard time transitioning from throwing on flat ground to getting on the mound and executing a bullpen session without discomfort in his ailing right shoulder.

The Red Sox might now be having a hard time of transitioning to the thought of their best pitcher — when healthy — returning for the stretch run.

Buchholz threw from 90 feet yesterday from flat ground before the opening of a three-game set with the New York Yankees at Fenway Park. But it’s more of the same in a process that has been one step forward and two steps back since the 28-year-old right-hander was sidelined in June by inflammation of the bursa sac in his right shoulder.

“We still hope he is out there for the better part of the remainder of the season,” said Red Sox general manager Ben Cherington. “For some reason, if that doesn’t happen, then we will just have to adjust. We’ve had guys step up before and we have guys who are capable of stepping up and being good starters and we will just have to see how that goes. We hope to have more clarity on that in the coming days and that will inform us to some degree.”

Before throwing from flat ground yesterday, Buchholz hadn’t thrown since feeling discomfort following a bullpen session in Oakland last Sunday. His scheduled bullpen session Tuesday at the All-Star Game in New York was scratched and he did not take part in Thursday’s voluntary workout.