When reverse synchronizing from your code, there are times when some Classes might be deliberately removed from your source code. Enterprise Architect's import source directory functionality keeps track of the Classes it expects to synchronize with and provides options for how to handle the Classes that weren't found. You can select the appropriate action so that, at the end of the import, Enterprise Architect either ignores the missing Classes, automatically deletes them or prompts you to handle them.

The dialog to delete Classes looks like this.

By default, all Classes are marked for deletion.  To keep one or more Classes select them and click on the Ignore button.