Dear Asif,
Regarding First Part of Your Query:
"Whether I can prosecute the company for dishonor of Cheque – A"
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
Facts about First Cheque from your Query:
Cheque – A was dishonored by bank due to "account closed"
You have issued notices to both the MD and the company
After receiving the notice, the MD sent a reply
MD asked for two months time and also issued a cheque – B
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
So, in first part of your query, you are asking about prosecution of the Company for the dishonour of Cheque – A, but your query is totally silent about the validity period and date of the Chque – A. Because on the said notice issued by you for the dishonour of cheque, and that too, after a period of TWO Months you can't initiate proceedings under 138 of NI Act for the dishonour of Cheque - A.
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
Issuance of Notice: Thirty (30) Days
Grace period : Fifteen (15) Days
Presentation of Complaint: Within Thirty Days after grace period of 15 days
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
Therefore, for this Cheque – A, now after a period of two month, can't initiate legal proceedings against the company under 138 of NI Act.
Regarding Second Part of Your Query:
" and simultaeneously issue notice for dishonour of Cheque B to invoke a new cause of action"
Exactly, you can now issue a notice (within 30 days from the dishonour of cheque) for the dishonour of Cheque – B, and within its limitation period you can initiate legal proceedings against the company and concerned person.
But don't forget to mention in your second notice about the issuance of Cheque – A, its dishonour, issuance of notice and the new facts about the present cheque – B.
One more important fact I want to point out to you, you are saying that Cheque – A is dishonoured due to "account closed", but your query is silent about the Cheque – B; whether this Cheque – B is of Same Account or any other account.
If the Cheque – B is also from same account, you can prosecute the company and concerned person (for both cheques) for the offence u/s 420 of IPC (cheating).