so why did that escape some scholars when it is so obvious?
Ibn Salaama, in his book الناسخ والمنسوخ في القرآن الكريم, page 119, says something that may explain why the scholars thought there is abrogation here. He writes, "Without this verse (52:21) mediation (الشفاعة) would have been void."
They must have thought that 53:39 deprives man from any reward he has not earned, and that 52:21 gives man a reward he has not earned. I beg to differ with both understandings.
Verse 53:39 sounds like it restricts what man will get by what he has earned, but the preposition لـ
(to) implies an entitlement
: that man has the right to claim what he has earned and to deny what he has not earned. It does not say that God will limit His judgment to that. It does not rule out any grace God may add, which man has not earned.
As for 52:21, it spells out one aspect of that Grace: joining righteous families together.
Neither verse talks about anybody putting in a good word for someone, which is what mediation (الشفاعة) is.