Salary issue

Hi I am from Mumbai. I was working one small multinational company from past 2 & half years. Because of my family issue I need to take sudden leave for 10 days and later need to extend it. However my company did not got agree on giving me more leave. So I resign from my post on immediate period. After resigning, I asked for my salary i worked for, I was on leave from 27th Jan So they need to pay me 26 days salary. So I got message from my COO that they will clear all my dues in 45 days & I got agreed for it. Now its above 45 days & till last week there where messaging me that he have informed the account dept. to release my salary. However later I found out there was new HR & she told me I have to pay 25000 to company because I did not serve notice period of 45 days. I checked my offer letter, It is mention that you have to serve notice period of 45 days, However it is not mention anywhere that "If any person do not serve notice period they will not get there salary for the days they have worked. Also I have all the messages & email from COO where he have mention of giving my salary. Now he is suddenly speaking HR language. I want to know can I report legal complaint against the company for not paying my salary.