Al-Khazraji, in his book نفس الصباح في غريب القرآن وناسخه ومنسوخه, volume 1, page 377, reports that Al-Hasan, Ad-Dhahhaak and `Ataa' all said that
was abrogated by
While Qataada said it was the other way around. An-Nahhaas agreed because, he said, 9:5 was revealed later than 47:4. Makki reported that Mujaahid said the same thing.
IMHO, there is no abrogation either way. Verse 9:5 orders several tactics toward hostile polytheists after the expiration of their peace treaty: killing them in battle, taking them as prisoners of war, placing an embargo on them, or stalking them. If they accept Islam, they are to be freed. The next verse makes it clear that they are not to be harmed if they cease hostility.
Verse 47:4 also orders two options when the battle is on: Killing the enemy, or taking them prisoners of war. Thus confirming 9:5. 9:5 adds two tactics that may avoid war: embargo and stalking. These do not apply to 47:4 which only talks about battle.
See also this related post.