Overview
It is now possible to stop sending notification on specific shops so that the CMS of those shops stops sending invoices to the end customer.
The use case is when the invoices sending is done outside myFulfillment & CMS but with a third tool.

If you want to stop all invoices on all shop, you need to deactivate the feed. The documentation is just to deactivate the invoices from a specific store.
Setup
From the home page, click on the top tab Integrations.
On the page reached, select the integration named System integration which has the type "System".
Once on it, select the Configuration tab
On the Customer invoice notification block, you have a drop-down field where you can select stores for which the invoice should be sent.
If none are selected, it behaves like all was selected. Selected stores appear with a light grey highlight.
On the screenshot below, orders from Store2 will not send invoices.