At the moment there is a bug where songs in the C3DB that currently have no attached customs will still trigger the duplicate filter. Fortunately it’s easy enough to work around, and I have done so. You should be able to (re-)upload the song now.
In the future, when you need to fix a custom, you can use your C3U file manager to upload a new version. Find the song in your file list, then select “Upload new version” from the action menu. The rest of the process will look familiar to you.
You are about to leave Rhythm Gaming World and access the external songs DB. While no song or file sold for commercially available videogames is hosted there and only fan generated content is allowed, Rhythm Gaming World has no direct control over the database and no files are hosted here. Alright, we had to made you aware of this, now you can visit the database!