where you can download Dr. Mustafa Zayd's book, "An-Naskh fi Al-Qur'aan", two volumes. This book is extensive and has plenty of footnotes.
What an encyclopedia that book is! More than 800 pages of extensive, well organized body of knowledge, with references cited for specific statements identifying the sources of various information. The book took 10 years of work.
The author says he is addressing abrogated verses in the Quran, precisely the thesis of this project. He describes the importance of the subject, and does not take abrogation claims lightly. He also addresses the question of whether there had been abrogated verses that were not included in the text. In addition, he contemplates a future book to deal with abrogation in the Sunna, and discusses how that situation is different from the Quran with sensible reasoning.
The Internet copy quoted above is actually a revised copy by someone who corrected the typos and other aspects, and annotated in the footnotes what he corrected. He mentions that the author followed Imam Malik's school of thought. He also mentions that the author's conclusion is that there are in fact abrogated verses, but that he reduced them to 6 verses.
Alas, the demeaning language used against those in the anti-abrogation camp is not avoided by the author, although he uses milder language than others. It seems that this style is the prevalent tradition in the theological community.
I can't judge the quality of the content until I read the book carefully, but based on what I have read so far, I believe that we have found a definitive reference on the subject.