We have already explained that one who has forgotten to count the Omer one day during the counting period may no longer count with a blessing on the subsequent days. The reason for this is because the Rishonim disagree as to whether the Mitzvah of counting the Omer is one long Mitzvah that spans along forty-nine days or every day of counting the Omer possesses its own Mitzvah. If we were to say that every day of counting possesses its own separate Mitzvah, even if one were to forget one full day of counting, he would still be able to continue counting the following night, for every day of counting is its own Mitzvah and there is no correlation between today’s counting and yesterday’s. Similarly, if one were to, G-d forbid, not don Tefillin one day, he would surely still be obligated to don then the next day, for there is no connection between today’s lack of donning Tefillin and continuing to fulfill this Mitzvah on subsequent days. However, if we say that the Mitzvah of counting the Omer is one long Mitzvah, if one forgets to count one day, he may no longer continue counting, for the moment he misses the counting of that specific day, he has lost the opportunity to fulfill the Mitzvah in its completion, and he no longer counts. This is indeed the opinion of the Ba’al Halachot Gedolot who holds that if one missed counting one day of the Omer, he no longer counts on subsequent days.
Halachically speaking, however, since most Rishonim disagree with the position of the Ba’al Halachot Gedolot, if one forgets to count one day of the Omer, he does indeed continue to count on the subsequent nights. Nevertheless, since the prohibition of reciting a blessing in vain is very severe as it entails uttering Hashem’s name in vain, we thus maintain that regarding the blessing of “Al Sefirat Ha’Omer,” the opinion of the Ba’al Halachot Gedolot must be taken into consideration and one who has forgotten to count one day of the Omer does not continue to recite the blessing upon counting on subsequent nights; rather, one continues to count without reciting a blessing beforehand, as per the rule of, “When in doubt, do not bless”.
Regarding our scenario, since we have just established that regarding the blessing we are concerned about the opinion of the Ba’al Halachot Gedolot, it would seem that if one is in doubt whether he counted the Omer or not (or if he is in doubt if he counted correctly, for instance, if one prayed alone, not with a Minyan, and is now uncertain if he counted the correct number), although he would continue to count on subsequent nights, he would nevertheless not be allowed to recite a blessing upon counting, for we must consider the opinion of the Ba’al Halachot Gedolot who holds that when one forgets to count one day, he does not continue to count the Omer.
However, halachically speaking, this is not so, for only if one is certain that he has forgotten to count one day do we say that he needs to be concerned about the opinion of the Ba’al Halachot Gedolot, and should continue counting without reciting a blessing. However, if one is uncertain whether he counted or not, he need not be concerned about the opinion of the Ba’al Halachot Gedolot, for in any case, most Rishonim disagree with his opinion. Therefore, the Halacha follows that if one is uncertain whether or not he has counted the Omer on the previous night, he will indeed continue to count the Omer on subsequent nights with a blessing.
Summary: If one is uncertain whether or not he has counted the Omer on the previous night, one should continue counting on subsequent nights with a blessing. Only if one is certain that one has forgotten to count one night, or that one has counted incorrectly, will one no longer recite a blessing upon counting on subsequent nights.