Here is the explanation of what I understood from your requirement. When you saved your file as .twbx then it only shows the columns which are present before saving the file and when you added any column in excel then it does not reflect on your worksheet. The same case is with .twb file with extract. But if you want that new column in Tableau, one simple method is to remove the extract from data source connection. This will automatically connect you to the main data source & will reflect the changes according to your database.
Hope this may work!
If you can give some more details, forum folks can advise you better solution.
What is your database? How do you combine different sources- (any common relationship?)
Are both databases coming from same server?
Please check Working with Multiple connections and