The last example Abu-Bakr Al-Hamdaani cites in his book الاعتبار في الناسخ والمنسوخ من الآثار, page 175, to prove that the Quran has abrogated Sunnas, is a narration that implies that the Prophet (PBUH) may have shaken hands with women other than of his family. This is when he had to accept their pledge of allegiance, per
He would place a cloth on his hand as he presumably shook theirs. The narration, by Ash-Shu`bi, is disconnected, Al-Hamdaani acknowledges, but then he says that if it is authentic then it gives evidence that his prior practice of never shaking hands with non-family women has been abrogated.
Those narrations all assume that accepting someone's pledge of allegiance must be done by shaking their hands, but God didn't say that! And verse 60:12 doesn't imply that either. Whatever method used to accept a pledge will fulfill the command in 60:12. Therefore, it is unnecessary to claim abrogation in this case.
That said, another narration Al-Hamdaani reports, narrated by Umayma bint Raqeeqa, makes it clear that the Prophet (PBUH) would not shake her hand or the hands of the other women who came with her to make the pledge; he simply said to them all that he accepts their pledge. That would count as an abrogation by him of his own practice, i.e., a Sunna abrogating another Sunna. Al-Hamdaani cites 15 more examples, on pages 175-190 of a Sunna abrogating another Sunna.