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We fixed a bug earlier today which caused the "local" vs. "server" prompt to not work properly when you chose "server": it would copy the data from the server, but leave you editing the old local data. In normal operation, you should only have to choose once and never again.

It's not necessary to close your document while syncing: OmniFocus individually tracks each change you make on each side, and applies merges those changes together when you sync.

(You can, of course, make nonsensical conflicting changes such as deleting an action on one computer while marking it complete on another. OmniFocus resolves these conflicts by taking whichever change happened last.)