Hi Thibaut,
The "Invoice Modified" Email Template can be disabled via the Setup > Email Templates page to prevent it from ever being sent: https://docs.whmcs.com/Email_Templates#Disabling_Templates

If you only want to disable the email in certain circumstances, the action hook system can be used to detect the conditions you require and abort email sending: https://developers.whmcs.com/hooks-reference/everything-else/#emailpresend