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I'm not aware of a convenient way to do what you ask with the sync mechanism if you've made other changes that you still wish to keep. "Convenient way" should be read here as "a way that I'm willing and able to describe in enough detail that I won't have to worry about you somehow further mangling your database in the process" :)

If the missing item is something that you didn't just create, you could probably retrieve it from a backup. You don't have to restore the backup to get something back, just browse in the Finder to the OmniFocus Backups directory in Documents, then double-click a backup that has a date suitable for finding your missing data. You can just drag and drop a copy of that project or action from the resulting window back into your regular library.

A rough sketch of how you might accomplish what you seek: immediately make a backup of your desktop database with the File->Backup Database command, to some place you could later easily find again. Then depending on your sync method, get rid of the sync database on MobileMe or in your Bonjour sync directory, and force the iPhone to do a sync, telling it to use the local copy if asked. That should repopulate the sync directory with the data from the iPhone, and you could sync from the desktop now (you want the server copy this time!), giving you back your database at some point prior to the erroneous deletion. Now you could open up that backup you squirreled away and group by changed to find all the stuff that you touched recently and set about recreating only the changes you wanted.