Muni Bhikanji studied the scriptures deeply during the chaturmas and at the end of the four months, he declared bravely, "Shravakasl you are right and we monks are misled. We are transgressing the code of conduct as prescribed in the scriptures. But you must not lose patience. I shall humbly place the whole matter before my guru. I am fully confident that he will take necessary steps to resolve this problem and re-establish the purity of conduct and thought in our order." The Shravakas felt relieved to hear these words from Muni Bhikanji and said, "We exactly expected this kind of ingenuousness from you." After the completion of the chaturmas, Muni Bhikanji returned to his guru in Marwar. On his arrival there, he found that two of his collegues (monks) who opposed to his new revolutionary thoughts of reformation had already apprised Acharya Raghunathji of the happenings at Rajnagar. This caused a dramatic change in the Acharyas' attitude towards Bhikanji.
Although Bhikanji gave him an honest and detailed account of what had transpired at Rajnagar, Raghunathji was unresponsive. The situation had deteriorated to such an extent that there was no solution for it. The guru did not agree with his suggestions to give up the laxity. At last Bhikanji thought that he should conform to the canonical code of ascetic conduct. Because of this, Bhikanji decided to leave the order. One day the inner conflict ended, when he, along with a few monks who also supported his view, separated from Acharya Raghunathji at Bagadi (Marwar) in V.S. 1817, Chaitra Sukla Navami.