Is there a way to remove all the subfolders of files?

I have an unofficial way to do this, using a private Retrobatch JS API.

You can add a JavaScript node after the read folder node and set the contents of the node to the following:

function processAsset(document, jsnode, asset) {
    asset.setOutputSubFolder(null);
    return true;
}

I’ll also attach a sample workflow:
RemoveSubfolderInfo.retrobatch (2.2 KB)

That should do the trick for now, though it might break in the future (it’s considered a private API, but I’ll try and add something equivalent to the API set at some point).