As I understand, your case is like this:
You've lent Rs 25 L to your friend by taking a Cheque from him and Promissory Note. As the cheque is bounced, you filed a case in your local u/s 138 of the Negotiable Instruments Act. In the court proceedings, your friend alleged that you stole his cheque and presented it for payment. Now your deposition is pending before the court.
You did not disclose the loan amount in your books and you have not filed your IT returns.
If my understanding of your case issue is right, the following issues merit consideration:
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1) If the payment of Rs 25 L to your friend is made by cheque/NEFT, you have a proof of payment. If, on the other hand, you gave the loan in cash, you may not be able to prove the loan. Even if you prove, your friend would have violated the provisions of Section 269S of the income Tax Act, under which borrowings in cash in excess of Rs 20,000/- attract penalty. If you gave the loan on or after 1st April 2017, you would have violated the provisions of Section 269ST of the Income Tax Act, whereby any transaction in cash for Rs 2 Lakhs or more is illegal and attracts penalty of equivalent amount.
2) If you are a business person, you need to maintain books of account reflecting the transaction. If you have not done it, you may do it now.
3) File all your returns and regularise your compliance with the provisions of the Income Tax Act, as otherwise the cost of non-compliance will be very high.You better take professional help for filing your IT returns properly.