As you have filed manually, you have to follow up with the concernede ITO to whom you had filed your return, for a new refund cheque, as it is likely that the earlier cheque has gone out of date.
Suggested action: You wrote on 20.3.12 to the ITO asking for a new cheque, explaining why the earlier cheque was not received,.Now please write a reminder letter immediately, enclosing a Xerox copy of your earlier letter (bearing the acknowledgement stamp), and obtain the office acknowledgement on this second letter too. In this second letter, give a reference to the first letter.
In all your letters that you take acknowledgement, please ensure that they bear the stamp of the ITO concerned along with the date.
If you dont get a reply even after a month for the second letter, you can have recourse to RTI. Find out from the ITO the designation of the officer in the income-tax department in whose name you should remit an IPO towards the cost of the RTI application. Your Income-Tax Officer is also your information officer. Address the RTI application to the same I-T Officer, attach copies of your earlier correspondence (asking for a new refund cheque) bearing the acknowledgement stamp of the office.
What to write in the RTI letter: Be very polite, and ask for information such as the details of the new refund cheque (issued in lieu of the original refund cheque returned undelivered due to wrong address), its date, amount, drawee bank, how the new cheque was sent to you (e.g. by speedpost/courier), the address to which the new cheque was sent to you, the date of sending the cheque, reference no. of the postal/courier service for the envelope, and the name of the person who signed the acknowledgement for having received the cheque.
It is important to be very polite and ask for information. You should not ask questions such as why the new cheque was not sent or why there was delay, etc.
On the RTI application, please also say that you want the reply by registered post and that the total cost of Rs 50/- for the RTI query (Rs 50/-) is being attached in the form of IPO no..... dated...... Please retain a Xerox copy of the IPO and deliver the RTI application to the same ITO and obtain their acknowledgement with stamp/date, on a Xerox copy of the application.
In the normal course, the I-T Officer is expected to give a reply within one month of receipt of the RTI query. If he does not, then he would be penalised. Hence most I-T Officers give priority to RTI queries and reply. In this case, since a replacement cheque has not been sent, he would ensure that a new cheque is sent within one month. If he does not, then you have a right to appeal to the next higher authority in the Dept. who could be an Asst. or Deputy Commissioner of Income-Tax supervising your ITO. That appeal has to be a similar RTI application along with a new IPO.
Still no reply?: You can appeal to the Income-Tax Ombudsman having jurisdiction over your area. You can obtain details from the dept. This appeal can be on a simple letter, giving all previous details of RTI queries along with copies of acknowldegements. The Ombudsman will ensure that you get your refund cheque.
My experience: I too did not get my refund cheque against a rectification application made by me, for several years. Finally I sent an RTI application and got the refund amount within one month, with interest. The ITO was very cooperative and knowledgeable about RTI matters.
Note: I am not a CA and what I have mentioned here is based on my general reading and actual experience. I hope you succeed too. Good luck.