Contact the support ninjas and they'll help you investigate the problem. 1-800-315-6664 or email
omnifocus-iphone@omnigroup.com
I've been using the iPhone app for many years, and it has never lost any of my data.
Omni Sync Server most certainly does work via 3G! I think perhaps you are confusing the Omni Sync Server (which is a web server available from anywhere on internet) with the Bonjour sync, which works only on a local network (which implies WiFi-only for the iPhone and iPad apps, but not for the Mac).
The Omni Sync Server is free and generally very reliable. While they did have a brief outage the other day, they've been doing better than some name brand web services like Dropbox and Netflix! Sign up at
http://sync.omnigroup.com