One who did not do hafrashat challa on dough may do so even on the resulting bread.[3] [4] However, your question is a good one. Should the challah be taken from the dough, the bread, both, or either?
One may not do hafrashat challa from one min (type) to apply to another, e.g., if two batches are made from different grains.[5] Are raw dough and baked bread made from the same grain considered to be one min in this regard? The Tur[6] discusses the case of one who mixed up loaves of bread, of which some had hafrashat challa, while some had not and thus cannot be eaten. How does he arrange to take challa from the loaves that were not covered by a hafrasha? One solution is to make an additional batch of dough that is enough to create a new obligation of hafrashat challa, connect it to the existing loaves, and then take challa from the new dough with a stipulation that the hafrasha applies also to whichever loaves require it. The Derisha[7] wonders why one could not suffice by preparing a small amount of new dough, which, upon being connected to the existing loaves, is enough to create an obligation of challa based on the combination with whichever loaves need a hafrasha. He answers that bread and dough are like two minim, which do not combine to create an obligation of hafrashat challa. Therefore, while the baked bread that previously required hafrashat challa still does, the new dough is exempt because of its small amount, and one cannot take challah from something that is not obligated in order to apply it to something that is obligated. However, if the new batch of dough is large enough to cause one to be obligated in hafrashat challa independently, the challa taken from it can also apply to the bread. Extending this concept to your case, the original dough ostensibly obligated you in hafrashat challa, and challa can therefore be taken from either the bread or the dough.
However, we must examine a few assumptions. First, it is not clear that all agree with the Derisha. The Hagahot Maimoniot[8] says that one cannot apply hafrashat challa from bread to dough or vice versa. However, that is a minority opinion, and the Challat Lechem[9] even limits it to an exceptional situation.
The truth is that the procedure of baking some of the dough and freezing the rest complicates matters in a manner that few seem to be aware of. The Shulchan Aruch[10] (based on a mishna[11]) states that if one makes enough dough for hafrashat challa with the intention of dividing it before baking into pieces that individually are too small for hafrashat challa, the entire batch is exempt from hafrashat challa. (Although the obligation begins at the time it is dough, this is based on the assumption that the future baking will be performed in a manner in which it is still obligated in hafrashat challa. In contrast, once the bread is baked, separating it into parts does not affect the obligation of hafrashat challa.)
If so, how do we ever do hafrashat challa, since our individual loaves are clearly less than the shiur of challa? One answer is that the aforementioned ruling refers to situations in which the dough is given to different people. In contrast, if one keeps all of the dough, since it is possible that the baked small loaves will be “reunited” later, it is considered one batch, and there is consequently an obligation.[12] Nevertheless, several poskim differentiate between levels of future connections of the loaves even when they are kept by one person.[13] This is not the forum for an in-depth analysis. The bottom line is that it is unclear whether there is an obligation of hafrashat challa when that which is baked immediately and that which is planned to be baked much later are individually “undersized.” (The obligation is even less likely when the later baking takes place after the the first loaves have been consumed.)
Let us consider various possibilities in your general scenario. If the amount that you bake in the first round is clearly not enough for hafrashat challa (e.g., if you broke up the dough into two equal sections), then because of the doubt regarding whether the two parts count as one batch, you should not make a beracha. (Those who prepare dough for two weeks of baking just so they can make a beracha are paying the price of creating a situation in which that beracha is questionable.) Regarding your specific question, regarding a case in which you did not do hafrashat challa right away, it is easier to rely on the aformentioned Derisha and to do hafrashat challa at the point when you remembered (without a beracha), taking the challa from either the bread or the dough. If this week’s batch is enough for an obligation and the leftover dough is smaller and thus possibly exempt, then according to some sources, taking challah from the possibly exempt dough to apply to the obligated bread is invalid. However, it is possible that the minhag follows the opinion that views the dough to be baked and that to be frozen as one batch if it is owned by one person, as many women take challa with a beracha even in this situation.[14]
In your case, the safest halachic idea is to bake the remaining dough (and freeze the bread) and put the batches together by having them touch, be in the same utensil, or by covering them together[15] for hafrashat challa. Another safe system is to take challa from the bread on the bread and from the dough on the dough (without a beracha, assuming each is too small for a beracha).