Menachos 66 records Abaye's opinion that it is a mitzvah to count both days and weeks of sefirah, which the gemara indicates was accepted l’halacha. Ameimar disagrees, and holds only the days but not the weeks need to be counted because “zecher l’mikdash hu”, the mitzvah of counting is only a reminder of the practice which was done at the time of the Bais haMikdash when an omer offering was brought.
Ameimar’s opinion is at first glance very difficult to understand – just because a mitzvah is only a zecher l’mikdash, why should the way in which it is performed change? For example, taking a lulav during 7 days of sukkot is only a zecher l’mikdash – no one holds that since it is only a zecher one needs to take only 2 minim and not 4. Why then should we dispense with counting weeks and only count the days of sefirah because it is a zecher l'mikdash?
R’ Yerucham asks why we do not recite two brachos on sefira, one for counting days and one for counting weeks, just as we recite two separate brachos on tefillin, one for the shel rosh and one for the shel yad. R’ Yerucham answers that the mitzvah of counting days is still Biblically in effect today and warrants a bracha; the mitzvah of counting weeks only applied when there was a Bais haMikdash, and hence in our times, when it is only a zecher, it does not warrant a bracha.
Why there should be a distinction between days and weeks is left as a “sod Hashem” by R’ Yerucham, but the Ohr Sameiach (Hil Temidim) reveals the secret. The gemara in Rosh haShana (5) writes that even though Shavuos is only a one day holiday, one has tashlumin for the korbanos of Yom Tov for seven days, just like other regalim. Since we count weeks leading up to the holiday, and the holiday is in fact called the “Holiday of Weeks”, it indicates that the period of time open to bring korbanos is one week. Even though we also count days, notes the O.S., we see from the gemara that the count of weeks specifically is associated with korbanos. Therefore, post-Bais haMikdash, this count is not Biblically mandatory.
Based on R’ Yerucham, the dispute in the gemara is clear. Abaye held that the count of weeks is Rabbinically in force even though there is no longer a Biblical obligation; Ameimer held that we are left only with the Biblical count of days but no count of weeks is required.
Most RIshonim do not accept R’ Yerucham’s split – either they hold that the count of both days and weeks is still Biblically mandatory (Rambam) or entirely Rabbinic (Tosfos). According to these approaches, further explanation of the gemara is needed.