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Does one fulfill 49 Mitzvos upon counting for 49 days or is it considered one single Mitzvah?
According to all opinions, each day of the count is a separate Mitzvah. This is similar to the Mitzvah of Tefillin, of which each day that one wears Tefillin he fulfills the Mitzvah of Tefillin and so too each day that one counts the Omer he fulfills the Mitzvah of Sefiras HaOmer.
 Likkutei Sichos 1/270
Background: There is dispute as to whether we consider the 49 days of Sefira as one unit of a Mitzvah, and hence if one day is lacking the entire Mitzvah is now forfeited, or whether one considers the Mitzvah as 49 separate Mitzvos, similar to 49 separate Mitzvos of donning Tefillin each morning. [see Halacha 19] Seemingly, according to the first approach that it is a single Mitzvah, a number of difficulties are raised, such as why one counts each night with a blessing, a total of 49 blessings, when in truth it’s only one Mitzvah. Likewise, one should not be allowed to count until the 49th night just in case one will miss a future night which will invalidate his Mitzvah retroactively? Rather the explanation is as follows: All agree that there is a new Mitzvah to count every night, however the dispute is whether the current day is dependent on the previous days count. According to the first opinion, each day is dependent on the previous day’s count in order for that days count to be Temimos. Meaning that if one did not count day 17 then he can’t count day 18, as the number 17 is missing from the 18th count. However, the counts of the previous days, from days 1-16 remain unaffected, being that they do not include day 17 that became invalid. The second opinion however holds that the Mitzvah of each night is completely independent of the previous nights, and the count on the 17th is not required to include within it the fulfilled count of any of the previous nights. [Likkutei Sichos 1/270; See also Yabia Omer 1/21; Piskeiy Teshuvos 489/22]