If I'm understanding you correctly, you have changes outstanding on both desktop and iPhone and don't want to lose any of them when you switch to Bonjour syncing over WiFi? Here's how I would do it:
On the desktop, do File->Back Up Database
Configure the desktop to sync via Bonjour, storing the database on the local machine
Now if you are going to use an ad hoc network to connect desktop and iPhone, set it up. Otherwise, make sure the desktop is connected to the wireless network and configure the iPhone to do so also. I'm not certain if you need to turn off the cellular data connection to force the iPhone to use WiFi -- I've got an iPod Touch.
On the iPhone, go to the Settings page in OmniFocus and set it to sync via Bonjour. Then you'll tap the broadcast settings button in OmniFocus' sync preferences on the desktop and capture the settings on the iPhone. If this doesn't work, and you can't "see" the desktop broadcasting its settings, you're not going to be able to sync. A failure probably means that you aren't connecting to the same network, or there's some device or software blocking traffic between the iPhone and desktop.
Now that you have the iPhone configured to sync via Bonjour/WiFi, have it do a sync. Tell it to keep the iPhone's database, which will propagate it to the server (desktop).
On the desktop, do a sync. Agree to download the server database and start syncing, or use the sync database (I forget what the exact language is this week). When that sync completes, both desktop and iPhone will have identical databases.
In the Finder, with OmniFocus already open in your newly synced database, double-click the backup file you made in the first step, which will get you another window. Go through and find the various changes you made since you last successfully synced the two devices together, and copy them over to the new database by dragging and dropping. You'll probably want to make some use of the sorting and/or grouping by added or changed features in both context and project mode to track down these changes if you don't remember where they all are. The lack of those features in the iPhone app means that it is probably easier to keep the iPhone version of the database even if there are more outstanding changes in the other version, simply because you won't have the tools to make sure you got them all if you keep the desktop version instead.
When you're doing moving data from the backup document, close that window so you don't accidentally put some changes in it thinking it is your live document.
If this seems confusing, you can always call up the support ninjas at Omni and they'll walk you through it.