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In addition to the sync info each of your devices uses, OmniFocus' sync depends on an extra server database that your devices all know to look at for updates. When Bonjour sync is turned on, OmniFocus on your Mac actually creates that extra copy of your data and fires up a web server on your local network. (It's completely replacing the sync server, in other words, and stores the "server" info separately from it's own info.)

On a purely technical level, yeah, this can work, but it's not really designed to be used this way and I can see problems happening down the line. Our sync server has one version of your data, the bonjour info has another version, and at some point the version you have on your device(s) isn't the one you want.

In general, OmniFocus expects you to pick the best sync method for you and to stick with it, not bounce around frequently. If "use bonjour unless I go on a trip, then switch to the Omni server" is the best work flow for you, that should work, but I wouldn't switch every day or multiple times a day or anything...