Cheyrou, already set to miss Sunday's Ligue 1 clash at Parc des Princes, has not sufficiently recovered from a thigh problem and will not make the squad for their last 16 cup tie on Wednesday.
Attacking midfielder Amalfitano has been suffering with knee pain and will be out of action for weeks.
"He will go to a recovery centre for 15 days in order to heal his knee because it has bothered him a lot in the past weeks," Baup told a news conference.
Third-placed Marseille, who trail leaders PSG by five points, will also be without suspended striker Jordan Ayew for the league match.
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