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Dr. Az-Zalmi, in his book التبيان لرفع غموض النسخ في القرآن, page 191, lists this case, that

was abrogated by the Jizya verse,


He says that claim was made by As-Suddi and Ibn Salaama who said that 3:111 was valid until the command came to fight the people of the Book. He refutes the claim on two bases,

1. 3:111 is about bearing abuse that does not escalate to war, while 9:29 is entirely about war, and
2. 3:111 is declarative; it cannot be abrogated.

He said As-Saawi and Ar-Raazi rejected the abrogation claim.

For:
As-Suddi,
Ibn Salaama.

Against:
At-Tabari, Qataada, Ar-Rabee`, Ibn Jurayj and Al-Hasan Al-Basri (implied, according to Dr. Zayd),
Al-Qurtubi (implied as he said that 3:102 was the only abrogated verse in Chapter 3),
As-Saawi, Ar-Raazi (according to Az-Zalmi),
Dr. Mustafa Zayd,
Dr. Az-Zalmi.

Dr. Mustafa Zayd, in his book النسخ في القرآن الكريم, volume 1, page 418 (item 588), quotes At-Tabari from his exegesis saying that the clause لن يضروكم إلا أذى (They will not harm you except an insult) in 3:111 is an Arabic literary style called الاستثناء المنقطع, such as when they say, ما اشتكى شيئا إلا خيرا (He did not complain of anything but good). That is, what comes after the exception is not included in what comes before it. In other words, what the clause means is, "They will not harm you. They can only insult you, e.g., with their blasphemous words).

Then Zayd wonders how can the pro-abrogation folk claim that the Jizya verse abrogated 3:111 when the latter promises Muslims that they will win the fight if they are fought?

I think Dr. Zayd misses the point here, made by the pro-abrogation folk, namely that the Jizya verse, in their interpretation, commands Muslims to start the fight against the people of the Book. It doesn't, of course, since the practice of the Prophet (PBUH) and the Sahaaba was the opposite. Islam went to Africa, the Indian subcontinent, Southeast Asia, and many more places without any fight. Muslims fought only those who fought their right to preach Islam to others, such as in Persia, Spain and Byzantine-occupied Syria.

What the Jizya verse commands is to collect a defense tax as compensation for Zakah, from people of the Book who are citizens of an Islamic country, and, if they don't, fight them until they do. And that is exactly what Muslims have done throughout their history. This is no different from Federal marshals in the USA who are legally empowered to fight citizens who refuse to pay taxes.