Hi Stephen,
Yes, that should work without issue. A rebuild is highly unlikely to fail, and if it does nothing should break. Your site will be down, but the data is safe in a persistent storage location (not in a docker container).
Taking a backup is a great idea (always backup) and yes, your uploads are not downloaded into the backup. Your database references the uploads on S3, and will continue to do so in the backup and if restored. As such, downloading them isn’t needed, they’re safe already in S3.
If anything goes wrong with the rebuild, post the log output here!