Athi Varadharaja is one among the 4 Brahma Kararchita Varadaja moorthies , carved out of Athi Tree by Vishwakarma in Kritha Yuga. This moorthi was the main deity (Moola Moorthi) in the Grabhagraha, i.e inside PunyaKooti Vimana, until early 16th century. Due to Muslim Invasions, to preserve the valuable moorthies , the Athi Varada was immersed inside Pushkaranai(Anatha Saravora) inside the temple premises secretively, such that only one family knew the exact place.
For nearly 40 long years, the temple had no moorthies in the grabhagraha and no pooja was being performed in the temple. The two brothers in Dhatacharya lineage,who were the Dharamakartha of the temple at that time and under whose authority the hiding of moorthy took place, passed away. Their two sons, after more than 40 years, tried vigorously to bring the moorthies back to the temple, to start the pooja again. With the help of a Madwa , the Utsava moorthies were brought back from Udayar Palayam forest and found their place inside the temple.
Unable to find the Athi Varadha, the authorities decided to place a Vigraha made of stone from the near by place called PazayaSeevaram (30 kms approx. from the temple). This moorthi is called DevarajaSwami and it is known to be Athri Rishi Kararchita moorthy. This moorthy resembled Athi Varadharaja and was present in a mountain called Padma Giri in Pazayaseevarm , where 3 rivers (Payasvini, Vegavathi and BahuNadhi) met forming a Triveni Sangama. This moorthy, called Devaraja, was brought to Kanchipuram and installed as moolamoorthi inside punyakoti vimana and the regular pooja started.
Around 1709 due to some reasons (which is unknown till the date) the Pushkarani was emptied and the Athi Varadharaja was seen lying inside. Then Authorities decided that this moorthi has to be taken out every 40 years for pooja for 48 days and again to be immersed in the kalyani for another 40 years and so on. This decision was based on the fact that, Kaliyuga pooja for Varadharaj is done by sesha devuru and Anatha sarovara has sesha devaru sannidhana , it is gods will that he immersed himself inside the Kalyani because of this very reason.