That was the case on Tuesday, when Beckett informed Francona of a stiff neck that prevented him from taking the ball in the opener of the Sox's three-game series against the Angels.
Right-hander David Pauley was enlisted from Triple-A Pawtucket to make the start. To make room for Pauley on the roster, utility infielder/outfielder Joe Thurston was designated for assignment.
With a flu bug spreading through the clubhouse in recent days, the Sox scratched Pauley from his start at Triple-A on Sunday in the event one of the Boston starters couldn't take the ball.
Beckett was one of the players feeling the effects of the illness, but just when that had subsided enough for him to stay on track against the Angels, the stiff neck came into play. It might be that the neck is related to the sickness.
"His neck got real stiff," Francona said. "Whether it's related or not, how do you know? We're not going to run him out there and have it potentially hurt his shoulder because he's got a stiff neck."
But Francona indicated after Tuesday's 7-6 victory that Beckett will go back into the rotation on his next scheduled turn, which is on Sunday against the Rays.
Making matters even more complicated for the Sox on Tuesday was the continued unavailability of catcher Jason Varitek, who has been struggling more than anyone else on the team with the flu. Reliever Manny Delcarmen was also sent home about an hour before Tuesday's game with flu-like symptoms.
Backup catcher Kevin Cash was in the lineup for the third straight day, though Varitek wouldn't have caught on Sunday with knuckleballer Tim Wakefield pitching.
Before being forced to scratch Beckett and bring up Pauley, the Red Sox were all but set to call up another backup catcher from Pawtucket. But they no longer have the roster flexibility to do that.
If Cash should suffer an injury, look for Dustin Pedroia of all people to step in.
"If we ever run into a problem, Pedroia says he can be the backup catcher," said Francona. "At this point, that was good enough for me. Once somebody says they can do it, they may not get a [chance to change their mind]. We'll get some equipment to fit him and he'll be all right."
Pedroia's catching history dates back to Little League and high school.
"I caught a lot in little league," Pedroia said. "My brother caught, so I was always around him. I think the last game I caught, I was in high school. It was all right. It was a lot different than the infield."
Ian Browne is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.