Here is what I posted several years ago :
The Rambam firmly construes Sefirat Ha'Omer as 1 Mitzvah. Sefer HaHinuch concurs with the Rambam's read. ... Case Closed.
But it is NOT closed Here is more information gained with a bit of persistence and a lot of assistance!
See Sefer Hamitzvot of the Rambam Mitzva 161 and his reference to Mitzva 140.
And From Micha Berger
shavuot/shav68-mt.htmIt's a machloqes. Rabbeinu Yerucham says that the qorban and counting weeks is one mitzvah, and counting days another. Therefore, counting weeks today is a derabbanan zeikher lamiqdash. The Rambam (asei 161) refers back to asei 140, counting yoveil, as well as points to the fact that there is only one berakhah to show that it's one mitzvah. He also notes that we do mention the weeks daily, unlike the Baal haMaor who only required numbering the week weekly.
In either case, R' "Meish" (Moshe) Taragin discusses it at length. Ayin sham.
The Rambam assumes that tefillah shel rosh rosh einah me'aqeves es shel yad and v.v. proves that they are separate chiyuvim. (Tekheiles and lavan within a single mitzvah of tzitzis is the exception.) I know this is the converse aand not the contrapositive, but does holding that counting days and counting weeks are mutually me'aqvos force one to count them as a single one of the 613?
And so the Beat goes on. The Count goes on, Too