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OmniOutliner by default will embed the file when you drag and drop it into the outline. If you drag and drop a folder, or hold down the control key when dragging and dropping a file, you will get a link which will go to the item instead of pulling the (possibly stale) data out of the OmniOutliner file. It sounds like you are using OmniOutliner as a file organizing tool, and for that you'll definitely want to do the control key trick when attaching files.

The OmniOutliner help for "attach file" covers this material well. You were embedding copies of the files in your outline, so when the external file changed, you didn't see the changes (and clicking on the external file in the finder took you to a different place).