Henrietta returned to France during the reign of Charles II for several reasons. One was the fact that she had never liked England to begin with, and the English didn't like her either.
Another reason was the fact that Henrietta spent a lot of time moping, so she wasn't much fun to be around. Charles II wanted to keep up a real court, and was depending on his mother to help him since his wife, Catherine of Braganza, was more or less useless. Henrietta's depression meant that Charles's mistresses became the true social leaders of the Court.
Henrietta may also have returned to France out of guilt over the unhappy marriage she had arranged for Minette. There had been many good offers for Minette after the restoration of Charles II, but Henrietta helped persuade Charles II to accept the Duke of Orleans's offer. The marriage was very unhappy, since Minette consoled herself elsewhere for her husband's homosexuality, which led to scenes and fights.
Henrietta left during a bad outbreak of plague, and promised Charles II to return. Both of them knew she was lying.
As for Charles II's children and their grandmother:
Henrietta helped raise the Duke of Monmouth, but unfortunately, she left Monmouth to be raised by servants in her household. As a result, Monmouth was not well-educated, and in adulthood, was easily persuaded to believe that he was legitimate and so forth.