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I had exactly the same issue when i was trying out the Omni server for the first time, and tried to publish a newly created file. The error messages implied that Mac Omni plan thought the file was already on the server.

Very helpful response from Omni's Aaron:

Go to "File" > "Save As" and save a new copy of your project file. By doing this, you're creating a new OmniPlan file with a new unique ID. We use unique IDs to keep track of projects on the server so in the event that someone on your team accidentally renames their project file the sync should still work.

With the newly saved file open, try to publish that to the server. If the publishing is successful, have all of your colleagues download the new project from the server.
Which worked v nicely.