Update documentation to reflect custom job behavior changes

Co-authored-by: mazhelez <[email protected]>

Author: Copilot

Scenarios/UpdateAlGoSystemFiles.md

@@ -24,6 +24,10 @@
 
 1. By default, this workflow will apply any updates to the **workflow files (in .github\\workflows)** or **system scripts (in .AL-Go)** from the template repository used to spin up the repository. If you want to change branch or template Url, you can specify the `templateUrl@branch` when you run the workflow.
 
+1. **Custom jobs behavior**: When updating system files, custom jobs are handled differently based on repository type:
+   - **Template repositories** (without `templateUrl` setting): Custom jobs are preserved and applied
+   - **Final repositories** (with `templateUrl` pointing to another repository): Custom jobs from the current repository are NOT applied to prevent persistence of jobs removed from the template
+
 ______________________________________________________________________
 
 [back](../README.md)

Scenarios/settings.md

@@ -408,7 +408,10 @@ In the `needs` property, you specify which jobs should be complete before this j
     strategy: ${{ fromJson(needs.Initialization.outputs.environmentsMatrixJson) }}
 ```
 
-Custom jobs will be preserved when running Update AL-Go System Files.
+Custom jobs will be preserved when running Update AL-Go System Files, with the following behavior:
+
+- **Template repositories** (repositories without a `templateUrl` setting): Custom jobs are preserved and applied during updates
+- **Final repositories** (repositories with a `templateUrl` pointing to another repository): Custom jobs from the current repository are NOT applied during updates to prevent persistence of jobs removed from the template
 
 **Note** that installing [apps from the GitHub marketplace](https://github.com/marketplace?type=apps) might require you to add custom jobs or steps to some of the workflows to get the right integration. In custom jobs, you can use any [actions from the GitHub marketplace](https://github.com/marketplace?type=actions).