[Lizard]

Yes, you'll generally get a new .zip file and a new .client with every sync.
(Which will happen every minute or so while you're actively making changes in OmniFocus.)
But they're only going to get automatically smooshed about once an hour.

So it doesn't necessarily sound like there's anything going wrong for any of you.

canadagoose: I'm not sure I understand your question about implementing an overwrite system.

EDIT: Some gremlin told me once upon a time that only the Mac smooshed your data, not the iPhone. This turns out to be lies, so I am removing my misinformation.