What is "Shetef Over"?
Rashi: It is flooding anger.
Radak: The place of Ninveh, which was mentioned, He will flood it once, and its place will be eradicated. It will not be recognized that there was a city there.
Malbim: The previous verse depicts Hashem as a fortress from affliction. He is also a flood to finish the affliction. He will eradicate the place from which the affliction came to the world (Eretz Ashur).
Why does it say "Kalah Ya'aseh Mekomah"?
Rashi: He will eradicate the place of the land. This refers to "va'Tisa ha'Aretz mi'Panav" (5).
Malbim: Refer to 1:8:1:3.
What is the meaning of "Yeradef Choshech"?
Radak: This is Po'el Yotzei Shelishi (one causes a second to act on a third party). Hashem causes darkness to chase the enemies. Darkness is a Mashal for a great affliction.
Malbim: Hashem made the Chidekel river flood Ninveh, and the entire city fled, as if their path is darkness and slippery and Hashem's angel chases them, like I explained above (refer to 1:1:3:1*).