The author means that popular sovereignty "undermined the Missouri Compromise" by indicating that it reopened debate over the border between free and slave states. Therefore, the correct answer is:
D. it reopened debate over the border between free and slave states.
Popular sovereignty allowed the settlers of a territory to determine whether they would allow slavery, which challenged the clear delineation established by the Missouri Compromise regarding free and slave states. This led to increased conflict over the status of slavery in new territories and states.