### Apache Airflow version

2.7.0

### What happened

On the DAGs page, the All, Active, and Paused counts include deleted DAGs. This is different from <= 2.6.1 (at least), where they were not included in the totals. Specifically this is for DAGs for which the DAG files have been removed, not DAGs that have been deleted via the UI.

### What you think should happen instead

Including deleted DAGs in those counts is confusing, and this behavior should revert to the previous behavior.

### How to reproduce

Create a DAG. 
Wait for totals to increment.
Remove the DAG file.

The totals will not change.

### Operating System

Debian GNU/Linux 11 (bullseye)

### Versions of Apache Airflow Providers

```apache-airflow-providers-amazon==8.5.1
apache-airflow-providers-celery==3.3.2
apache-airflow-providers-cncf-kubernetes==7.4.2
apache-airflow-providers-common-sql==1.7.0
apache-airflow-providers-datadog==3.3.1
apache-airflow-providers-elasticsearch==5.0.0
apache-airflow-providers-ftp==3.5.0
apache-airflow-providers-google==10.6.0
apache-airflow-providers-http==4.5.0
apache-airflow-providers-imap==3.3.0
apache-airflow-providers-microsoft-azure==6.2.4
apache-airflow-providers-postgres==5.6.0
apache-airflow-providers-redis==3.3.1
apache-airflow-providers-salesforce==5.4.1
apache-airflow-providers-slack==7.3.2
apache-airflow-providers-snowflake==4.4.2
apache-airflow-providers-sqlite==3.4.3
```

### Deployment

Astronomer

### Deployment details

_No response_

### Anything else

I suspect the issue is with [DagModel.deactivate_deleted_dags](https://github.com/apache/airflow/blob/f971ba2f2f9703d0e1954e52aaded52a83c2f844/airflow/models/dag.py#L3564), but I'm unable to verify.



### Are you willing to submit PR?

- [ ] Yes I am willing to submit a PR!

### Code of Conduct

- [X] I agree to follow this project's [Code of Conduct](https://github.com/apache/airflow/blob/main/CODE_OF_CONDUCT.md)

return redirect(self.get_default_url())
def action_has_dag_edit_access(action_func: Callable) -> Callable:
    """Decorator for actions which verifies you have DAG edit access on the given tis/drs."""
    @wraps(action_func)
    def check_dag_edit_acl_for_actions(
        self,
        items: list[TaskInstance] | list[DagRun] | TaskInstance | DagRun | None,
        *args,
        **kwargs,
    ) -> Callable:
        if items is None:
            dag_ids: set[str] = set()
        elif isinstance(items, list):
            dag_ids = {item.dag_id for item in items if item is not None}
        elif isinstance(items, (TaskInstance, DagRun)):
            dag_ids = {items.dag_id}
        else:
            raise ValueError(
                "Was expecting the first argument of the action to be of type "
                "list[TaskInstance] | list[DagRun] | TaskInstance | DagRun | None."
                f"Was of type: {type(items)}"
            )
        for dag_id in dag_ids:
            if not get_airflow_app().appbuilder.sm.can_edit_dag(dag_id):
                flash(f"Access denied for dag_id {dag_id}", "danger")
                logging.warning("User %s tried to modify %s without having access.", g.user.username, dag_id)
                return redirect(self.get_default_url())
        return action_func(self, items, *args, **kwargs)
    return check_dag_edit_acl_for_actions
class SlaMissModelView(AirflowModelView):