The Rambam in Hilchos Teshuvah 1:2 says (talking about the times of the Beis Hamikdash) ??? ????? ?? ??? ??? ???? ?? ??? ????? ????? ?????? ???? ???? ?????
Whether it was known to him or unknown to him, everything is atoned for with the goat of Azazel, provided he did Teshuvah.
This would imply that Teshuva must be done even if individual who committed the aveiros never found out about them.