Is communication via WhatsApp between a male teaching assistant and female students to answer academic questions considered a "khalwa" (impermissible private meeting) and thus makes the work unlawful?

If your conversation with female students is for a beneficial purpose, and your answers are limited to their questions, then there is no sin upon you and your earnings are permissible, given the existence of legitimate Islamic guidelines for communication between a man and a foreign woman. What you are doing is not considered an unlawful khalwa (private seclusion).