If a person did not count the Omer one night, and the following day he remembered his mistake only during the period of Ben Ha'shemashot ("twilight"), which extends for approximately 13.5 minutes after sundown, he should count without a Beracha. Halacha treats the period of Ben Ha'shemashot as a "Safek" a situation of uncertainty, as we are unsure whether to consider it daytime or nighttime. As such, if a person did not remember to count the Omer until Ben Ha'shemashot, he must count without a Beracha, given the possibility that night has already begun and he has therefore missed an entire day of counting.
The question arises as to whether the person in this case may continue counting with a Beracha that night. Seemingly, we should apply to this situation the concept of "Sefek Sefeka," or a "double doubt." Firstly, it is possible that the period of Ben Ha'shemashot is still daytime, in which case he did not miss any days of counting. Additionally, it is possible that Halacha follows the position of Rabbenu Tam (France, 1100-1171), who held that one may continue counting with a Beracha even if he missed a day of counting. At first glance, the combination of these two factors should allow the individual to continue counting with a Beracha.
The "Bet David," however, rejected this rationale, claiming that this situation does not qualify as a true "Sefek Sefeka." In his view, the status of "Ben Ha'shemashot" is by definition one of doubt, and thus even if we accept the possibility that it constitutes daytime, we must still treat it as a questionable period, and it therefore cannot be taken into account to create a "Sefek Sefeka."
Hacham Ovadia Yosef, however, in his work Yabia Omer (in vol. 4 and in vol. 10), disagrees. Firstly, he denies the distinction between the "Safek" status of Ben Ha'shemashot and other situations of Halachic doubt, and he thus maintains that this case indeed qualifies as a legitimate "Sefek Sefeka." Moreover, Hacham Ovadia notes, we must take into account as well the view of Rabbenu Tam that Ben Ha'shemashot begins later in the evening. According to Rabbenu Tam's position, when the person counted during what we consider Ben Ha'shemashot, it was still definitively during the daytime, and the counting was therefore perfectly valid. Hence, the person may certainly continue counting with a Beracha.
However, Hacham Ovadia adds one condition to this ruling. Namely, the individual must ensure henceforth to count only when nighttime has fallen, and not during the period of Ben Ha'shemashot. If he continues counting with a Beracha on the assumption that his counting during Ben Ha'shemashot occurred during the day, he cannot then treat Ben Ha'shemashot as nighttime at some later point during the Omer, as this would be self-contradictory. Therefore, a person in this case must ensure to count every night after the conclusion of Ben Ha'shemashot, preferably no earlier than 20-40 minutes after sundown.
Summary: If a person did not count the Omer one night and remembered the following day only during Ben Ha'shemashot the 13.5-minute period after sundown he should count without a Beracha, and may then resume counting as normal with a Beracha that night. Throughout the rest of the Omer, however, he must make a point to always count no earlier than 20-40 minutes after sundown.
