What happens if my visa expires while my passport is at the Immigration office?

You do not need to leave your passport at Immigration.

You only bring it for your biometrics appointment and you take it back with you immediately afterward. As long as your visa extension was submitted before your current visa expired, you will not incur any overstay fees.

Immigration counts the submission date, not the approval date. So even if your extension is still being processed when your original visa expires, you are legally covered.