When there is a contradiction between the Shulchan Aruch Harav and his siddur,which one does the poskim use?
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Although there was some initial confusion on this question among some poskim, because the Siddur was printed during the Alter Rebbe's lifetime, where as the Shulchan Aruch was only printed after his passing (even though he wrote the Shulchan Aruch when he was 26 years old), his children write that the Siddur was written later than the Shulchan Aruch, therefore it is the Mishna Achrona and what is considered his psak.
This is the Chabad practice as well.
Sources: This letter from the Rebbe in the appendix to Sefer Haminhagim (Chabad) (English), the letter preceding that, the Tzemach Tzedek's chiddushim on Mishnayos, 46b, the introduction to the new print of the Shulchan Aruch HaRav, references ad loc., and elsewhere.