In general, we always recommend regenerating paths and refreshing references if you are experiences issues like this. Here is an example of how to resolve this:
1. Make a minor change to the subflow in ARD; even moving a block slightly will do.
2. Save the subflow.
3. Repeat for all of the subflows.
4. In the main flow, you will receive a notification saying a subflow update is available. Click the notifications panel like so:
5. Now hit the ‘Reload direct subflows’ button:
6. Now you should be able to generate Automation from the master flow that takes into account the subflows.