Generally, you will need to file an IR21 (and withhold all payments to the employees) tax clearance with IRAS for non-Singapore citizen employees (i.e. foreign or Singapore Permanent Resident employee) who resigns or will be away physically in Singapore either for overseas posting or otherwise. This will includes all foreign employees under work permit, special pass or employment pass.
However, for foreign employees who are physically away from Singapore specifically due to the current COVID-19 restriction and are performing remote working outside Singapore, employer will be exempted from filing IR21 tax clearance. You will need to ensure that these foreign employees remain as your employees during the period of absence and are away due specifically to COVID-19 situation. The foreign employees must also hold valid work passes, continue to receive salaries during the period and they will return to work in Singapore after the COVID restriction is lifted.