When Not to Upload:
If you have already uploaded all your source files, including the scene file, textures, light caches, etc., but then want to make a change to the scene file, you DO NOT need to re-upload textures, light caches, etc., a second time. Simply make the necessary scene change and re-upload the new/updated scene file.
NOTE: When uploading via Web Uploader, there is a checkbox to overwrite the pre-existing file (if they have the same name).
It is recommended that you upload the NEW scene file with a new unique name.
When to Upload:
The only time you would have to upload new textures, for example, is if you make a scene change that uses a brand new texture that is not already uploaded.