### 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)

DagParsingSignal,
    DagParsingStat,
)
from airflow.dag_processing.processor import DagFileProcessorProcess
from airflow.jobs.dag_processor_job_runner import DagProcessorJobRunner
from airflow.jobs.job import Job
from airflow.models import DagBag, DagModel, DbCallbackRequest, errors
from airflow.models.dagcode import DagCode
from airflow.models.serialized_dag import SerializedDagModel
from airflow.utils import timezone
from airflow.utils.net import get_hostname
from airflow.utils.session import create_session
from tests.core.test_logging_config import SETTINGS_FILE_VALID, settings_context
from tests.models import TEST_DAGS_FOLDER
from tests.test_utils.config import conf_vars
from tests.test_utils.db import clear_db_callbacks, clear_db_dags, clear_db_runs, clear_db_serialized_dags
TEST_DAG_FOLDER = pathlib.Path(__file__).parents[1].resolve() / "dags"
DEFAULT_DATE = timezone.datetime(2016, 1, 1)
class FakeDagFileProcessorRunner(DagFileProcessorProcess):
    
    
    def __init__(self, file_path, pickle_dags, dag_ids, dag_directory, callbacks):
        super().__init__(file_path, pickle_dags, dag_ids, dag_directory, callbacks)
        
        readable, writable = multiprocessing.Pipe(duplex=False)
        writable.send("abc")
        writable.close()
        self._waitable_handle = readable
        self._result = 0, 0
    def start(self):