What can centrally manage S3 backups from Windows EC2 servers?

Before picking an agent, check whether you actually need individual files stored as S3 objects. If the folders are on EBS volumes, AWS Backup can manage scheduled snapshots through backup plans. That changes the unit of backup from a folder sync to a volume snapshot.

AWS Backup also supports searching supported EBS backups and restoring individual items, including from NTFS volumes. Check the current requirements and restore workflow against your setup, especially where the folders are mounted. It may be a simpler fit if the goal is recovery rather than having a browsable S3 copy.

Systems Manager is worth a look if the scripts themselves are working and the main pain is managing them. You can schedule PowerShell on the instances centrally, track execution and use monitoring and alerts for failures.

That keeps the S3 sync approach rather than replacing it with a backup product. You would still need to maintain the script and make sure it reports failures clearly.

For an agent and dashboard, check out Veeam or MSP360. Plenty of commercial backup packages can target S3, but I'd compare the Windows agent, central scheduling, failure reporting and restore workflow before choosing.

Also check pricing for the number of servers and the features you need. Being able to send data to S3 isn't quite the same thing as being able to find and restore a particular file easily.

Another option is to keep the existing sync script but manage its configuration with Ansible, Puppet or Chef. That can make schedules and settings consistent across the servers without manually editing each one. You'd still need a separate way to monitor jobs and verify restores.