Baked Shiur Challah without separating Challah:
Baked the entire Shiur Challah whole: If one kneaded a Shiur Challah of dough and forgot to remove Challah from it prior to baking, then if the Shiur Challah dough was baked in its full size without being distributed to smaller portions, one is to simply remove the Challah from it after it is baked.
Baked portions of the Shiur Challah-Eretz Yisrael: If the dough was distributed into smaller portions, such as one baked many loaves of bread from the Shiur Challah dough, then although it is not necessary to separate Challah from each individual baked product, nevertheless there is a difference in law between Eretz Yisrael and the Diaspora in regards to how the separation must be done, if it requires “Min Hamukaf”. In Eretz Yisrael one is required to place all the pieces of dough and baked goods in front of him and near each other [i.e. Min Hamukaf] and only then is he to separate Challah from [either the leftover dough, or] one of the baked products, on behalf of all the other pieces that were part of the original Shiur Challah. It is however not necessary for the pieces to touch each other [or be in the same vessel], and rather so long as they near and close by to each other, it is considered Min Hamukaf. Nevertheless, since there opinions that rule Min Hamukaf is defined as having all the pieces touch each other, and other opinions rule it means having all the pieces in a single vessel, therefore one who is G-d fearing should suspect for both opinions and [initially] place all the pieces together in a vessel and have them touch each other while in the vessel.
Baked portions of the Shiur Challah-Diaspora: The above only applies in Eretz Yisrael, however, in the Diaspora, if the Shiur Challah dough was distributed into smaller portions and baked one can simply remove Challah from any leftover dough, or any of the baked portions, and have it count on behalf of all the portions of that dough. It is not even initially necessary to place the doughs/baked goods in a vessel or near each other [i.e. Min Hamukaf] in order to validate the Hafrashas Challah on behalf of all the pieces that were part of the original Shiur Challah. Rather, even though the pieces have not been joined together one may separate from one piece on behalf of them all, being that they were already joined and obligated in Challah while they were still dough. Nevertheless, it is a Midas Chassidus to be stringent and separate Min Hamukaf even in the Diaspora, and so is the custom. One is to be stringent even in this case according to all the opinions of “Min Hamukaf” and place all the pieces of dough/baked products in a single vessel and have them touch each other and only then separate Challah.
Bedieved-If one did not separate Challah Min Hamukaf: Even in a case that separating Min Hamukaf is required from the letter of the law, such as by Challah of Eretz Yisrael, it is only required Lechatchilah/initially. However Bedieved if one already separated challah not Min Hamukaf, then it is nevertheless valid and one is not required to re-separate the Challah Min Hamukaf.
The law of the pans and oven: In all cases the pans and oven used for the baking of the dough remain Kosher once Challah is removed, even though it was baked in it while it was still Tevel, prior to having its Challah removed.
 Michaber 327/5; Admur 457/6-12
 Michaber 323/1; Admur O.C. 457/8 and 11-12
 Admur 457/8; Mishneh Challah 1/9; 2/8; Rambam Bikkurim 5/13
The reason: As Challas Eretz Yisrael is only removed Min Hamukaf, meaning near each other, as explained in Michaber Y.D. 323/1. [Admur ibid]
 Admur ibid; Bach 457/3; Peri Chadash 457/1; Rosh Challah 4
 1st opinion in Admur 457/11; Nekudos Hakesef Y.D. 326; Sefer Hateruma 81; Semag 141
 2nd opinion in Admur 457/11; Tosafus
 Admur 457/11; See Admur 457/12 that applies these two stringencies even to the Diaspora. Thus, although in 457/8 Admur clearly writes that it is not required for the doughs to be touching, and no mention of having them in a single vessel is made, nevertheless in 457/12 he explains that it is proper to do so, in order to suspect for the above opinions. Vetzaruch Iyun
 Admur O.C. 457/7-9; Michaber/Rama 323/1
 Admur 457/7; Rama 457/1; Rosh 3/6; Ran
 Admur 457/7
 Admur 457/9 and 12; Taz 457/5; Semag 141; Rosh Beitza 1/13; Ran
 Admur 457/12 and 260/5 in parentheses; Rashbatz 2/291-7
 Admur 457/12
 Admur 457/13; Chok Yaakov 457/6; Rashbatz 2/291-7; Michaber 331/25 regarding Teruma; See Tzemach tzedek Y.D. 235/1