Bangalore Development Authority is the Planning Authority for Bangalore Metropolitan area.
In the comprehensive development plan the Hoskote taluk comes under BDA which would grant approval of residential Industrial & Commercial Layouts in favour of House Building Co-Operative Society (HBCS) / Institutions and individuals and also approval of development plan for Group Housing Scheme.
In your case there is a clause already imposed the building plan should be approved by BDA, it would be improper to obtain plan approval from Panchayat board.
The builder in order to somehow promote the sale has suppressed the fact and obtained approval from panchayat officials by bribing them.
The power to approve plans by panchayat board was repealed very long ago.
The sanctioning of building plan by the village panchayat secretary is ultra vires.
If there is a possibility to get the plan regularized by BDA at this stage, you may try for that .
Even if you skip this party, this problem will persist until you are not clearing it or getting it regularised.