[DerekM]

It sounds like you're saving as opml instead of the OmniOutliner 3 format. There is a bug in the opml parsing that will duplicate links every time you save and reopen the file if the app is set to auto create attachments from urls.

If you want to keep saving as opml, then you will need to turn on this setting which is general tab of the OmniOutliner preferences. If you save it as the oo3 format instead, then you can leave the setting on. Unfortunately, there's no automatic way to remove all the duplicates.