We're working to resolve issues with syncing. Meanwhile, here are some ways to reduce conflicts and data loss until we can push out those fixes.
1) Make sure your .ofocus file is smooshing properly. When all your clients are synced up, you should only have a couple .zip files in your OmniFocus.ofocus file. Follow the steps
here on one Mac and sync it, choosing "Local" if you get prompted. Then resync all your other machines and choose "Server" to get the smooshed file.
2) Leave OmniFocus running on your Macs as much as possible. They create a bunch of somewhat bogus updates on launch that can cause conflicts.
3) Sync every time you start and stop using OmniFocus on a particular Mac or iPhone.