Files
Suppose that /foo/src contains only A.c and that /foo/dest contains both A.c and B.c. And suppose I run the following command:
rsync /foo/src/ /foo/dest
Will rsync erase B.c?
Folders
Now suppose that /foo/src contains the directory A with some files inside it and that /foo/dest contains both directories A and B, each with some files inside of them. And suppose I run the following command (the -a option includes -r, recursive):
rsync -a /foo/src/ /foo/dest
Will rsync erase B and its contents?