Question: [Friday, 19th Mar Cheshvan, 5781]
I made my regular Challah recipe which has more than enough flour to separate Challah with a blessing and somehow I forgot to separate the Challah and only realized after I began baking the first batch. What do I do and how do I separate the Challah?
There is no need to worry. In such a case, you should simply wait until the Challah in the oven is ready to be removed and then prior to placing the new batch in the oven you should place all of the dough and baked Challah next each other and separate a piece from one of the doughs on behalf of all of the other doughs and baked bread. There is no need to wait until all the bread is baked to do this and there is likewise no need to separate a piece from each individual loaf. Nonetheless, it is best to initially place all of the dough and baked Challah in a single vessel and have them touch each other. [While technically you can wait for all the dough to be baked and only then separate in the above method, I would not suggest to do so as you may come to forget and therefore the earlier you do so the better.]
Sources: Regarding the order of hakafah when one forgot to separate prior to baking see our article: https://shulchanaruchharav.com/halacha/forgot-to-separate-challah/
Regarding that one can do Hakafah of dough and baked bread together if they each have Shiur Challah [or if they were all part of the same Shiur Challah] and thereby do not require Tziruf [as in our case] See: Admur 457:16; Shach in Nekudos Hakesef Y.D. 326 in great length and that he vehemently proves that the concept of Hakpadah by two species only applies to Tziruf and not to Hakafah.