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Have a look in your Documents folder for a folder called OmniFocus backups. In there, there should be a file called OmniFocus Prior to Resynchronizing on <date and time>.ofocus-backup. Whenever OmniFocus replaces its database with another one, it makes such a backup. Use File->Revert to Database Backup to restore that database, and when you are sure that it is what you want, use File->Replace Server Database to push it to the server. Then you will need to resync your iPhone, and when asked whether to keep the device database or the sync database, choose the sync database. Anything you did on the iPhone will be lost.

If you did a bunch of stuff on the iPhone you wish to keep, use File->Back Up Database to make a backup copy of your database before using File->Revert to Database Backup. After the backup has been restored and you've got the iPhone syncing, you can double-click (in the Finder) on the backup you just made and drag and drop from one window to the other to copy over any missing items.

Omni should consider putting in some language in the setup screens for sync that walks you through setting things up in the proper order when you get a new gadget. There's an easy way, and a hard way, and it's all too easy to choose the hard way when you don't know that the order matters!