[Black Tiger]

You go wrong at step 3.
The file won't be replaced that way, only the title will be replaced!!. You should not edit and change. You should just upload the new file, then choose the old file and delete it.

In the download pages you don't see "junk v1.0" anymore, nor can you download it.

Well... you could download it if you knew the correct filename, like 11145-junk.zip because the way you use it, only description gets overwritten and new file will be uploaded, but old file won't be deleted.
An edit function is to edit things, not to replace files. I even wonder if you get a new filedate then on your new file.

So now I understand better what kind of problem that you have, and you caused it yourself by doing step 3 and 4 instread of just upload the new file.

With this explanation now I understand why you can't delete the files that way. Now I hope Jelle can fix you with a solution.
Otherwise maybe you can use the find function but for that you need SSH access on the server.