We do have our uploads folder in a different location, /wp/uploads and had the issue. Rolling back to 4.5.8 got the downloads working again, but some of them have disappeared from the Downloads. They still work, but we have no way to update them now.
Both are HTTPS on my client’s site. They do have WordPress in a subdirectory, so the WordPress Address is different from the Site Address.
I’ll add that their site is now working properly on version 4.4.11.
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This reply was modified 4 years, 7 months ago by synapdylan.
I have a client site on Apache that was experiencing this with version 4.4.6 as well. Rolling back to version 4.4.4 seems to have fixed it.
In their case requests were being redirected to the protected file despite the “Redirect to file” option not being checked.