Facebook and Instagram Messenger are two different applications and they are not synced. This means that if you delete a message on Facebook Messenger, it will not be deleted on Instagram Messenger and vice versa. If you want to delete a message on both Facebook Messenger and Instagram Messenger, you need to delete it on each application.
Video – How To Unsync Facebook And Instagram Messenger
And that’s it! You have now unsynced your Facebook and Instagram Messenger accounts. If you ever want to sync them again, just follow these same steps.