I'm lost regarding the timeline. Was Younshin pregnant with Seo Juntae before the switch occurred between Hwang Hyeondo and Gwon Yohan? I wonder who is Juntae's biological father.

Yes, FAKE Hwang Hyeondo never know it until Seo Youngshin told him at the end. She also doesn't know that FAKE Hwang Hyeondo is actually REAL Gwon Yohan. She knows that FAKE Gwon Yohan is dead, because of the CCTV recording (proof). So, Seo Juntae's biological father is Gwon Yohan (FAKE Hwang Hyeondo).