By the very act of you issuing stop payment instructions to your bank, you have demonstrated that you did not accept the terms of agreement. Hence you have revoked the proposal(agreement of sale) by your act of stop payment of cheque (sec 6 (3) of Indian Contract Act)
Kindly also issue notices to builder that you are not interested to purchase the property and hence the agreement for sale is deemed to be cancelled.
If the seller sends you a return legal notice, you can always revert by pointing to the legal defects in his title.
No issues are likely to arise as you have prevented yourself from being cheated and you have complied with the provisions of Indian Contract Act for revocation of agreement of sale (i.e stop payment of cheque and also issuing notices).
Hope this information is useful