For a new project I imported 2 tables into the DDT. No stored procedures were imported. No views were imported.
I made sure that object name history was clear.
I edited these two tables. I also added two new tables to the DDT.
The object name history was looking good and ready for a deployment.
I deployed my changes to the database. At this point, I have four tables that should be showing up in the table list with my changes. They did!! Suh-weeet! This is great stuff...and so easy. 
Maybe too easy!?!
At the time I did not know it, but ALL stored procedures were dropped from the database. ALL views were dropped from the database. Only table schema should have been altered in the DB, right? Did I blow by some checkbox somewhere that says, "Drop all SPs/Views"? What configuration of the DDT would cause this behavior?
Please help me so that I am not dropping things every time I deploy changes to my database. 
Thanks,
Bill