Hi,
I am currently employed at a great company that sponsors my E3 visa. It is still in the pending process (currently at: Request for Evidence), but I just received a family emergency back at home (Taiwan).

I need to leave the United States February, but I don't know if my visa will complete the process by then, will I be able to leave and come back to work?

I am a dual citizenship of Taiwan and Australia, I enter the United States with Australian passport.

As long as you maintain employment with this sponsor, you will be fine. If you leave US permanently, your status will be terminated.