I paid an advance for a flat but the builder hasn't given me the allotment letter even after a year. They now want all original documents for a cheque. Is it safe to give them the originals? What if the cheque bounces? Can I file a case with just copies

You can take legal action against your friend for non-payment. You can file a civil suit in a court of competent jurisdiction to recover the amount owed. You can also approach the credit card company to report the fraudulent transaction and seek their assistance in recovering the amount.