Functions disappear from app after arm template deploy

#### Investigative information

Please provide the following:

- Timestamp: 2022-03-02
- Function App version: 4
- Region: West-Europe

#### Repro steps

Provide the steps required to reproduce the problem:

1. Create a:
- Linux function app in a consumption plan
- Set `WEBSITE_RUN_FROM_PACKAGE` to 1
2. Deploy the code using Azure Pipelines (zip deploy)
- This changes the `WEBSITE_RUN_FROM_PACKAGE` setting to `https://{storage_account}/azure-pipelines-deploy/{package_name}?{SAS token}`
3. Re-deploy the arm template

#### Expected behavior

The functions should still exist in the function app, and the function app should still work

#### Actual behavior

The setting `WEBSITE_RUN_FROM_PACKAGE` is reset to 1 and the functions disappear from the app.