According to the original novel, The Hermes has two engine systems; Attitude Thrusters (which use classical oxygen/hydrazine-based rocket fuel) and an Ionic-Thrust engine (which use electrostatically-charged argon to create thrust and is going to be used to get them home safely).
When it becomes clear that the ship has missed its rendezvous point with Mark, they use the attitude thrusters to close the gap. At no point is it suggested that the ion engines would run low on fuel, just that they would be ineffective, given their low rate of thrust:
“Vogel,” Lewis continued, “how far can we deflect in thirty-nine minutes with the ion engines?”
“Perhaps five kilometers,” he radioed.
This is explained in a little more detail a few paragraphs later:
“The launch missed badly,” Venkat said, looking past Mitch to the screens beyond. “The intercept distance was going to be way too big. So they’re using the attitude adjusters to close the gap.”
“What do attitude adjusters usually do?”
“They rotate the ship. They’re not made for thrusting it. Hermes doesn’t have quick-reaction engines. Just the slow, steady ion engines.”
Since the main ionic engines haven't dramatically affected their orbit (nor run low on fuel) it should be a vanishingly simple matter to use them to un-correct the earlier course-correction and keep them on their planned Earth-Mars cycler trajectory.