All filestorage is done on the cloud server, files can only be accessed through the domain model.
You could create a microflow which deletes System.Filedocuments, but make sure that when you used the System.Filedocument as a generalization to remove these objects also.
A file is deleted when the record is removed.
Advice is to make your own entity which inherits from System.Filedocument.
Delete the invoice documents and Mendix will take care of the rest.
If running on premise or local you can actually remove the files from the deployment folder/data/files but that will corrupt the state of the data, you will get error messages when you open documents from Mendix that are deleted from disk.