we deleted all transients. As far I can tell we just deleted revisions and transients with that optimization plugin. So when we deleted the transients as told with downnload monitor plugin the downloads we had fixed were unuseable again with no file path.
So we ended up publish all downloads by hand. You might check if you delete transients that it might remove the file reference, but maybe it’s just our WordPress setup that we use (with a lot of custom code)…