It is entirely possible that you were running a very outdated version of PHP and your hosting provider has upgraded you silently due to security concerns.
My quick research reveals you might be hosted on inmotionhosting.com so please check your email to see if that’s the case and try to find your access details.
Take a look at https://wordpress.org/plugins/ilab-media-tools/ – I haven’t used it personally, but they do seem to support your use case with a paid plan.
The other option I see is for custom work to import your S3 media back into the WP Media Library and then set up a plugin that offloads back to S3 using WP’s folder structure.
Have you recently run a WordPress Update or made any other changes?
Do you have a backup by any chance?
Thanks @aytac, let’s continue the discussion over at GitHub.
