What is the meaning of "ha'Refa'im Yecholalu"?
Rashi: Gehinom, which is Merafeh (softens) people, its seven Chalalim (hollows, i.e. chambers - Sotah 10b) (refer to 26:5:2:1).
Ibn Ezra: Even ha'Refa'im, who are dead, Hashem will revive them under the water and those who dwell on the land. This refers to seeds.
Malbim #1: Ha'Refa'im are the dead who descended to the grave and were buried in the depth close to the Tehom - the water of the Tehom goes to there. So they will be born a second time to receive their reward and punishment.
Malbim #2: This is a claim against his opinion that the Ma'arachah determines everything; a Rasha with a good Mazal succeeds, for Hashem will not change the Ma'arachah. Hashem could punish Resha'im without changing nature! Refer to 26:5:2:2.
Where is "mi'Tachas Mayim v'Shochneihem"?
Rashi: It is in the depth of the depths.
Malbim: Hashem can take ha'Refa'im from under the water and punish them. I.e. He can make water float on the place of the Resha'im, like the days of the flood, and wipe out the Resha'im in it.
