### Apache Airflow version

2.5.3

### What happened

When a DAG is removed from a zip in the DAGs directory, but the zip file remains, it is not marked correctly as inactive. It is still visible in the UI, and attempting to open the DAG results in an `DAG "mydag" seems to be missing from DagBag.` error in the UI.

The DAG is removed from the SerializedDag table, resulting in the scheduler repeatedly erroring with `[2023-04-12T12:43:51.165+0000] {scheduler_job.py:1063} ERROR - DAG 'mydag' not found in serialized_dag table`.

I have done some minor investigating and it appears that [this piece of code](https://github.com/apache/airflow/blob/2.5.3/airflow/dag_processing/manager.py#L748-L772) may be the cause.

`dag_filelocs` provides the path to a specific python file within a zip, so `SerializedDagModel.remove_deleted_dags` is able to remove the missing DAG.

However, `self._file_paths` only contains the top-level zip name, so `DagModel.deactivate_deleted_dags` will only deactivate DAGs where the zip they are contained in is deleted, regardless of whether the DAG is still inside the zip.

I can see there are [other methods that handle DAG deactivation](https://github.com/apache/airflow/blob/2.5.3/airflow/models/dag.py#L2945-L2968) and I'm not sure how these all interact but this does seem to cause this specific issue.

### What you think should happen instead

DAGS that are no longer in the DagBag are marked as inactive

### How to reproduce

Running airflow locally with docker-compose:
- Create a zipfile with 2 DAG py files in in ./dags
- Wait for the DAGs to be parsed by the scheduler and appear in the UI
- Overwrite the existing DAG zip, with a new zip containing only 1 of the original DAG py files
- Wait for scheduler loop to parse the new zip
- Attempt to open the removed DAG in the UI, you will see an error



### Operating System

Debian GNU/Linux 11 (bullseye)

### Versions of Apache Airflow Providers

_No response_

### Deployment

Official Apache Airflow Helm Chart

### Deployment details

_No response_

### Anything else

If I replace the docker image in the docker compose with an image built from this Dockerfile:

```
FROM apache/airflow:2.5.3
RUN sed -i '772s/self._file_paths/dag_filelocs/' /home/airflow/.local/lib/python3.7/site-packages/airflow/dag_processing/manager.py
RUN sed -i '3351s/correct_maybe_zipped(dag_model.fileloc)/dag_model.fileloc/' /home/airflow/.local/lib/python3.7/site-packages/airflow/models/dag.py
```

The DAG is deactivated as expected

### Are you willing to submit PR?

- [X] 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)

query.delete(synchronize_session="fetch")
        session.commit()
    def _log_file_processing_stats(self, known_file_paths):
        """
        Print out stats about how files are getting processed.
        :param known_file_paths: a list of file paths that may contain Airflow
            DAG definitions
        :return: None
        """
        
        
        
        
        
        
        
        
        headers = ["File Path", "PID", "Runtime", "# DAGs", "# Errors", "Last Runtime", "Last Run"]
        rows = []
        now = timezone.utcnow()
        for file_path in known_file_paths:
            last_runtime = self.get_last_runtime(file_path)
            num_dags = self.get_last_dag_count(file_path)
            num_errors = self.get_last_error_count(file_path)
            file_name = os.path.basename(file_path)
            file_name = os.path.splitext(file_name)[0].replace(os.sep, ".")
            processor_pid = self.get_pid(file_path)
            processor_start_time = self.get_start_time(file_path)
            runtime = (now - processor_start_time) if processor_start_time else None
            last_run = self.get_last_finish_time(file_path)