The following is a list of the chapters of The Alter Rebbe’s Shulchan Aruch that are not extant:
Chapters 132 - 154
Chapter 157
Chapters 169 - 173
Chapters 175, 176
Chapters 208 - 211
Chapters 216 - 241
Chapter 304
Chapter 322
Chapters 409 - 428
Chapters 530 - 581
Chapter 630
Chapters 632 - 635
Note that while The Alter Rebbe’s Shulchan Aruch ends at chapter 651, the Shulchan Aruch of Rabbi Yosef Karo ends at chapter 697.
Additionally, the chapters on Hilchos Sukkos (625 - 651) are missing many Halachos as well as chapters.
There is also no section on Even HaEzer.
Finally, the section of Yoreh Deah of the Shulchan Aruch of Rabbi Yosef Karo has 403 chapters while The Alter Rebbe’s Shulchan Aruch is missing the vast majority of those chapters. The following is a list of the chapters we do have.
Chapters 1, 2
Chapter 18
Chapters 23 - 26
Chapters 30 - 33
Chapters 183 - 191