Like most things related to tech, we can't really say without a lot more detail: specs, size of sites, empty space on server etc etc.
Enhance is a paid product and has very good support. You should open a support ticket with them with all the info you can give and they may want SSH into the server. They will be your fastest way to resolve this.
That said have you verified your S3 settings are correct and checked whatever messed up interface AWS has that might have restrictions on what devices or IPs can upload?
