Thank you very much for your explanation.
Yes, yEd essentially overwrites existing files when saving changes. More precisely, yEd writes a changed diagram to a temporary file and if writing finishes successfully, moves the temporary file to the original file. This is actually a sensible thing to do, because if yEd was writing straight to the original file, an error during writing would mean that you not only lose your changes but the original file as well.
If SharePoint cannot handle this workflow, this is a shortcoming of SharePoint and you should file a request for enhancement with SharePoint.