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Each dough that is rolled for Matzah baking customarily contains less than Shiur Challah. Practically, due to this, Hafrashas Challah is never done prior to baking. After the baking, some Hashgachas join a required amount of baked Matzah into a vessel and then separate Challah with a blessing. Others, leave this Mitzvah for the buyer to perform. It is incumbent upon the buyer to check the box of Matzahs that he purchased to verify their status of Hafrashas Challah.
How to remove Challah from the Matzahs: If one’s Matzahs did not have Challah removed from them by the bakery, then one is to enter all the Matzahs into a single vessel [such as a single bag], for a total of Shiur Challah [approximately 2 kilo] of Matzahs. One says a blessing and then breaks off a Kezayis piece of Matzah on behalf of all the Matzahs in the vessel. One then says Harei Zu Challah and wraps up the piece and discards it into the garbage. If all the Matzahs cannot fit into one bag/box, then one is to repeat Hafrashas Challah for each bag/box, making sure they each have Shiur Challah [at least 2 kilo] in each one.
Forgot to remove Challah from the Matzahs: If it is already Shabbos or Yom Tov and one forgot to remove Challah from his Matzahs, then if they were baked in the Diaspora, one may eat the Matzahs. He is to leave a little piece from each Matzah remaining, and then after Yom Tov he is to separate Challah from all the pieces together. [If, however, the Matzahs were baked in Eretz Yisrael, then he may not eat the Matzahs, or separate Challah, until after Shabbos or Yom Tov. Rather, he should borrow Matzah from a neighbor.]
 See Admur 456:3 for a dispute and final ruling and custom
The reason: The reason for this is because dough which is larger than Shiur Challah cannot be completely kneaded at the same time. [Admur ibid]
 See Admur 457:2 and 6
 Admur 457:6
 In general we measure the flour alone, which is 1666.6 kilo for removing Challah with a blessing. [Shiurei Torah 3:1] However, baked Matzah, which contains also water, is not 100% flour, and hence one must add to the Shiur. However, see Piskeiy Teshuvos 457 footnote 1 and 27
 Admur 457:6
 Rama Y.D. 322:5
 See Admur 457:11-12; Piskeiy Teshuvos 457:5
 Admur 457:11
 Admur 260:5; 339:7; 524:1