[bug] Removing a route does not delete the API Gateway resource

### Steps to Reproduce
- Create a Chalice CDK app
- Add a route in `runtime/app.py`:
```
@app.route('/test', methods=['GET'])
def test_method():
return {}
```
- Run `cdk deploy` - the new `/test` resource shows up in the API Gateway console
- Remove the code snippet above
- Run `cdk deploy`

### Expected Outcome
The `/test` resource is deleted. Calling it returns the default API-G response:
```
{"message":"Missing Authentication Token"}
```

### Actual Outcome
The `/test` resource remains in API Gateway. When you try to call it, the following is returned:
```
{"Code":"MethodNotAllowedError","Message":"Unsupported method: GET"}
```

Reproduce the issue in a Chalice CDK app by adding and then removing the `/test` route in `runtime/app.py`, running `cdk deploy` after each change, and checking the API Gateway console. Investigate how route resources are synchronized during deployment; done means the removed `/test` resource is deleted and requests return `{"message":"Missing Authentication Token"}`.

Written by the indexing model from the issue text.