Just as a matter of being mentioned without any principle need look after:
Note sure whether a "bug" or setting issue: currently it's not possible to overwrite media-files without first removing/changing existing links to them on pages (which is of course good on one hand) and such needs to be done via ftp if wishing to avoid much work in editing links back and forward on pages to the file to upload it via media-manager. There is a setting of "looking whether file is used" to avoid deleting when used, yet overwrite might be (good) a different issue.