I know it is an old thread, but I came across this one when I was facing the same problem.. Someone might still benefit..
Here is what worked for me:
When you right click on the DB project in VS you get the ‘Publish Database’ dialog. You setup the target server connection and choose the correct database.
Then click on the ‘Advanced…’ button to open up the ‘Advanced Publish Settings’.
1) Uncheck - 'Block incremental deployment if data loss might occur' checkbox.
2) Check - 'DROP objects in target but not in project'
Click on OK button.
Then click on Generate Script button in order for the publish script to be generated.
You could save these settings to a profile file if you want to generate the script frequently.