Even though we reject the opinion of Rabeinu Yerucham that distinguishes the sefirah count of weeks as being only a zecher l’mikdash from the count of days, which is a Biblical obligation, that does not necessarily mean the count of days and weeks should be viewed as a single unit. While Ameimar’s opinion in Menachos 66 to count days and not weeks clearly separates between the two, it is unclear how to interpret Abaye’s position that both the count of days and weeks are obligatory. Does Abaye reject Ameimar's fundamental point that these two counts are separate mitzvot, or does he agree that the count of days and the count of weeks are separate obligations, but holds that both still apply in our time?
The Bais haLevi suggested that if one forgot to count a day of sefira, one may still count the units of weeks at each week's end, i.e. one may count day 7, 14, 21, etc. with a bracha. Clearly, the assumption of the Bh”L is that the count of days and the count of weeks function as separate units, and losing the opportunity to fulfill one with a bracha does not affect the opportunity to fulfill the other.