Dr. Mustafa Zayd, in his book النسخ في القرآن الكريم, volume 1, page 461 (item 469), writes that some have said that
was abrogated by
He found that claim in At-Tabari's exegesis. He dismisses the claim quickly on the basis that it is statement of fact stating an event that had happened, so can that possibly be abrogated?
I think that whoever made the claim was thinking that God has changed His ruling about People of the Book from expulsion to paying the Jizya. If that's what he thought, it demonstrates once again the misunderstanding many scholars had about the Jizya verse. Jizya is a defense tax that is collected in lieu of Zakah, from People of the Book who are citizens of a Muslim country. That's all it is. The Jizya verse orders the collection of this tax by force if necessary. It is only fair that non-Muslim citizens who are equally protected by the Muslim authorities contribute to their defense which is carried out mostly by Muslim citizens who also pay the Zakah.
That said, there are situations where non-Muslim citizens cause so much sedition that it is better to expel them in order to save bloodshed. That is what 59:3 was about. It was about Banu An-Nadheer, who were expelled from Medina for the sedition they were causing. A similar ruling was made by Umar later against the people of Najraan.
Thus, the two verses together make the following consistent statement,
"
People of the Book who are citizens of an Islamic country are entitled to defense just like Muslim citizens and thus must pay a tax in lieu of the Zakah that Muslims pay, toward the defense budget. If they refuse, they are fought for it. If they cause too much unrest, the Muslim ruler may expel them from the land in order to keep order and save bloodshed."