If one baked bread on yom tov in Eretz Yisroel (from dough kneaded prior to Yom Tov) and relized when the bread was still in the oven that he forgot to take off challah, must the bread then be considered muktzah? If indeed it is muktzah, would one have to leave it in the oven the entire time even until it burns or could one save it and take it out?
Based on what the Ramah writes in SA Siman 457:1 and SA Horav #16), there is a way to take Challa on Yom Tov: you could make a new dough (make the size of one Challah, because your going to have to eat that bread on that same day, per Mogen Avraham 506:11) bake it and AFTERWARD do צירוף כלי (put the Erev YT breads and the new bread in one utensil) and remove Challah from the NEW bread.
I wrote the bulk of this immediately after the question was posted several months ago, but I decided not to post it as it is sort of a long comment rather than a definitive answer. After I was reminded of this question by a recent post, I decided I might as well post my comments here. CYLOR, as usual.
If someone kneaded dough on Yom Tov of Pesach, and it became tamei, the opinion of Rabbi Eliezer in the Mishna (P'sachim 46a) is that the dough should be baked before challah is separated so that the challah doesn't turn into chametz. R' Eliezer holds that this is not afiya shelo l'tzorech prior to the separation of challah. Rabbeinu Baruch writes that the challah is muktza only after it is separated, since it is not fitting to be eaten in its state of tumah (Sefer HaT'ruma, Hil. Challah, § 84).
This seems to imply that, binidon didan, the fact that challah has not yet been separated does not intrinsically make the bread muktza. The question remains whether the bread is muktza because it may not be eaten on Yom Tov. Seemingly, the bread would be muktza because it would not be considered a davar shenigmar bidei adam since it cannot be made edible until after yom tov (so we can expect that asach da'tei minaihu) (Mishna B'rura, 310:19).
The bread seemingly may not be baked because, in this case, it would seem to be afiya shelo l'tzorech, as it may not be eaten on Yom Tov. Additionally, it seems that it may not be left to burn because of you cannot burn challah on Yom Tov (Shabbos 24b; Rashi, P'sachim 46a).
Assuming one could not apply the solution described in Meir Zirkind's answer, it would seem that the bread would need to be removed from the oven kil'achar yad. However, it may be logistically difficult to remove bread from a hot oven kil'achar yad; ironically, R' Moshe Feinstein is quoted as saying that it is questionable whether even moving an item backhanded qualifies as kil'achar yad (Igros Moshe OC vol. 5, 22:8).
It is further questionable whether one would be allowed to remove the bread in a normal manner, thus violating the d'rabbanan of muktza, in order to avoid cooking the bread, which would constitute a biblical prohibition. This seems to be related to the topic explored in the sugya of hidbik pas batanur (Shabbos 4a; see here and here for some discussion of relevant points).
Being that you are allowed to bake bread on Yom Tov, it would follow that you are allowed to do anything you can to eat the bread, including taking off challah, (because without taking off challah the bread is tevel). This is provable from Pesachim 36b/37a: "...Beis Hillel permit the baking of 'pas aveh' on yom tov... what is 'pas aveh'? 'pas merubeh'", i.e. a lot of bread, implying even an amount that would be chayav in challah. It would therefore follow that the bread is not muktzeh, being that is is indeed usable- all you need to do is take challah. (For more information on taking challah on Yom Tov, see Pesachim 46a/b.)