### 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)

failed_task_instance.dag_id,
                failed_task_instance.task_id,
                failed_task_instance.run_id,
            )
            if failed_task_instance.duration:
                fails_totals[dict_key] += failed_task_instance.duration
        
        def grouping_key(ti: TaskInstance):
            return ti.dag_id, ti.task_id, ti.run_id
        mapped_tis = set()
        for _, group in itertools.groupby(sorted(task_instances, key=grouping_key), key=grouping_key):
            tis = list(group)
            duration = sum(x.duration for x in tis if x.duration)
            if duration:
                first_ti = tis[0]
                if first_ti.map_index >= 0:
                    mapped_tis.add(first_ti.task_id)
                date_time = wwwutils.epoch(first_ti.execution_date)
                x_points[first_ti.task_id].append(date_time)
                fails_dict_key = (first_ti.dag_id, first_ti.task_id, first_ti.run_id)
                fails_total = fails_totals[fails_dict_key]
                y_points[first_ti.task_id].append(float(duration + fails_total))
        cumulative_y = {k: list(itertools.accumulate(v)) for k, v in y_points.items()}
        
        
        y_unit = infer_time_unit([d for t in y_points.values() for d in t])
        cum_y_unit = infer_time_unit([d for t in cumulative_y.values() for d in t])
        
        chart.create_y_axis("yAxis", format=".02f", custom_format=False, label=f"Duration ({y_unit})")
        chart.axislist["yAxis"]["axisLabelDistance"] = "-15"