Although the restaurant company has recently added many new

You just can't make or break a question on this kind of pronoun reference. Yes, you will see questions on GMAT with this kind of ambiguity (if you call it so), but there will be other deciding factors on these kind of questions.

The key word here is 'and' .. clearly signifies that the pronoun it's signifies the restaurant company and not country.

Although the restaurant company has recently added many new restaurants across the country and its sales have increased dramatically, its sales at restaurants open for more than a year have declined.
A. the restaurant company has recently added many new restaurants across the country and its sales have increased dramatically, its
B. the restaurant company has recently added many new restaurants across the country and its sales increased dramatically, its
C. many new restaurants have recently been opened across the country and its sales increased dramatically, the restaurant company’s
D. having recently added many new restaurants across the country and with its sales increasing dramatically, the restaurant company’s
E. recently adding many new restaurants across the country and having its sales increase dramatically, the restaurant company’s

This is the problem. Actually I was seraching a logical reasoning of not considering the first "its" referring to country. Can we say that as "its" coming after "and", so we can say with surity that the ancedent is restuarant not the country?? Similarly can we say that had there been no "and" between "country" & "its", then could have said that "its" referring to the "country".

I just want such kind of logic.

Hussain15, I agree with your view. I think that "its" refers to company on the basis of parallel structure with and.