Acquired property without full payment

I had a sale deed between a builder and me for an apartment in bangalore. I have made complete payment and wanted to sell it to a third party. As the buyer wanted to get loan from bank, I made an assignment agreement in favour the party. The agreement said, the builder can directly register the flat in favour of 3rd party, with myself being an confirming party/witness. However, the builder allowed the buyer to register the flat without my knowledge. Now I have received half payment from the buyer's bank and for the remaining, we agreed to have it paid within 3 months and I got PDCs for that. Now I am worried that the PDCs might get bounced. What do I do now. Can I make some kind of agreement which states the above and have it registered?