The sins we beget during morning and night get destroyed during the morning and evening sandhyavandanams, respectively. Swami Desikan had stated in Aparadha Parihaara adhikaaram of Srimad Rahasyatrayasaaram that atonements are for the sins that we commit intentionally. Please explain this.

There are certain mantras in sandhyvandanam that eradicate the sins we commit unknowingly. Atonements are the only solution for the sins we do knowingly.
Notes:
Elders have said, performing sandhyavandanam does not yield benefits but not performing it, will yield sin.
Sandhyavandanam will eradicate the sins that we commit unintentionally, while sins committed intentionally can be removed only through an atonement.