I have found the issue. In AX while using dixf its checking zipcode based on zipcode, country in csv but its not considering city. So its inserting first zipcode that its finding and city attached to that is getting Updated. I made a fix for that by writing job and updating LogisticsPostalAddress record(city,zipcode fields) for that Customer based on csv.
Job I wrote
gets city,zipcode, state, country from csv and finds zipcode (logisticsaddresszipcodetable) by using state,zipcode,country,city.
Same for city i found using state, zipcode, city, country.
Then i updated it in LogisticsPostalAddress Table for that customer.