Initially, the repository module utilized it's own file upload mechanism, and because at the time, there was no secure file storage solution built into the core, the repository module injected a Guid into the filename to 'psudo' secure it. When the core added secure file storage, that mechanism was no longer needed, but to prevent breaking all of the existing modules out there, support for the default upload method was retained.
If you edit your form.html file and simply change all your [FILE] and [IMAGE] tags to [URLCONTROLFILE] and [URLCONTROLIMAGE] respectively, then you will be using the core URL control to upload your files and their filenames will not be mangled. Then, when you update a file, the original file will be overwritten but the filename will remain the same and your external links will not be broken. NOTE: This change will only work for new files uploaded after changing the tokens. The existing files will remain mangled and the repository module can tell by the filename format how to retrieve the file when a user clicks on the download link.
However, I believe if, after you change the tokens, you simply go back and EDIT each item, resaving it will save it without the Guid, but I'm not 100% sure.