Not in the GUI I’m afraid, but if you simply FTP it to the right place with the same name (exactly) then it will be over-written.
If it is significantly different also delete its corresponding thumbnail version. A new one will then be automatically created from the new full-size image.
By the way, regarding
I’m doing a lot of uploading of media that for whatever reason isn’t in my media folder.
Are you sure they are not there? Have you tried ticking the “Unused files” options on Administration > Media? That displays any media items that exist in your folder, but do not exist as media objects in your GEDCOM data (i.e. are not “linked” to anything).