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The original Omer was an offering of newly cut barley.
So what happened during the Shmitta year when there was no harvest? Presumably this offering was not brought?
Was there still a biblical requirement to count the days and weeks like we do now? (Some say the mitzvah we keep now is only Rabbinic).
There was a korban omer even during shemitah. (Otherwise, how could one have eaten from chodosh in chutz la'aretz?) It came ideally from the "sefiach" (self-seeded produce); though if that wasn't available, it was imported from Suryah, or, if still necessary, planted in Israel and offered on the Altar (but not eaten by the priests). As such, all the related commandments were still applicable including sefirath ha'omer.
From Wikishiva :
מכיון שדין "מנחת העומר" לבוא מן התבואה החדשה, הרי שבשמיטה היתה מנחת העומר צריכה לבוא מספיחי תבואה שגדלה בשביעית.
לצורך מנחת העומר היה צריך להתיר את שריפת קומץ המנחה הקדוש בקדושת שביעית, חרף איסור הפסד פירות שביעית.
בשנת השמיטה היו בית הדין שוכרים שומרים שישמרו על הספיחים המיועדים למנחת העומר, "ואותן המעות שנותנים להם בשכרם (מתרומת הלשכה) הוא כאילו קונים בו העומר ושתי הלחם ... אם לא מצאו ספיחי תבואה בארץ ישראל, היו מביאים מסוריה; לא נמצאה בסוריה תבואה הראויה לעומר, מותר לזרוע תבואה לצורך העומר בארץ ישראל. "מנחת עומר" זו אמנם היתה קרבה על גבי המזבח, אך לא היתה נאכלת לכהנים, הואיל והבאתה היתה כרוכה בדחיית איסור זריעה בשמיטה.
Since the omer offering must come from new grain, therefore it needed to come from the self-seeded growth of the sabbatical year. It was necessary to allow the burning of the kometz of the sabbatical produce in spite of the general prohibition of destroying sabbatical produce. During the sabbatical year, the court would hire watchmen to guard the self-seeded growth designated for the Omer offering... If they found no self-seeded growth in the land of Israel, thye would bring from Suryah; If they also found no fitting grain there, then it was permitted to plant grain for the purpose of the Omer in the land of Israel in which case it was offered on the altar but not eaten by the priests since its offering was bound with the overriding of the prohibition of planting during the sabbatical year.
See also, Yerushalmi Shekalim 4:1 15b, Rambam Hilchos Shekalim 4:5 (and Hilchos Kiddush Hachodesh 4:15), and Meiri on Shekalim 4.
