Depending on the facts of the case, if the notice was properly served in the name of the proprietorship concern itself, the possibility of using Section 319 Cr.P.C. could perhaps have been explored during the pendency of the trial proceedings in the court to add proprietor as an accused. However, if the notice was not served in the proper name of the proprietorship concern itself, then even Section 319 Cr.P.C. would have been difficult to apply during trial too (since notice to the correct party is a necessary ingredient of offence under Section 138 of the Negotiable Instruments Act).
In any case, now that it appears from your question that the accused has already been acquitted (and the trial has completed) on the ground that he was not the proprietor, now it may not be possible to file a fresh case on the proprietor at such a late stage since the time periods mentioned in Section 138 would have already expired (you have mentioned in the title of the question that a period 2 years has elapsed).
But, you can still file a civil suit for the recovery of the amount due from the real proprietor of the proprietorship concern, if it is not beyond the limitation period of 3 years. Even if the limitation period has expired, depending on the actual facts of your case, it may perhaps be possible for you to take help of Section 14 of the Limitation Act ("Exclusion of time of proceeding bona fide in court without jurisdiction") for filing the civil suit.
Dr. Ashok Dhamija is a New Delhi based Supreme Court Advocate and author of law books. Read more about him by clicking here. List of his Forum Replies. List of his other articles. List of his Quora Answers. List of his YouTube Videos.