### 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)

Stats.incr("dag_processing.sla_callback_count")
        
        
        else:
            self.log.debug("Queuing %s CallbackRequest: %s", type(request).__name__, request)
            self._callback_to_execute[request.full_filepath].append(request)
            if request.full_filepath in self._file_path_queue:
                
                
                
                self._file_path_queue = collections.deque(
                    file_path for file_path in self._file_path_queue if file_path != request.full_filepath
                )
            self._add_paths_to_queue([request.full_filepath], True)
            Stats.incr("dag_processing.other_callback_count")
    def _refresh_dag_dir(self):
        """Refresh file paths from dag dir if we haven't done it for too long."""
        now = timezone.utcnow()
        elapsed_time_since_refresh = (now - self.last_dag_dir_refresh_time).total_seconds()
        if elapsed_time_since_refresh > self.dag_dir_list_interval:
            
            self.log.info("Searching for files in %s", self._dag_directory)
            self._file_paths = list_py_file_paths(self._dag_directory)
            self.last_dag_dir_refresh_time = now
            self.log.info("There are %s files in %s", len(self._file_paths), self._dag_directory)
            self.set_file_paths(self._file_paths)
            try:
                self.log.debug("Removing old import errors")
                DagFileProcessorManager.clear_nonexistent_import_errors(file_paths=self._file_paths)
            except Exception: