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Can you try to append the Ulysses project extension ".ulys" to the folders? The folder should be converted to a Ulysses project after changing the extension.
All Ulysses projects are stored as folders -- if you Ctrl-click a project file and select "Show Package Contents", you'll see the project contents (this is also useful if you ever want to recover texts and notes from a Ulysses project without the app). By appending the extension to the folder, it remains a folder, but is associated with Ulysses and the project should be opened with the app.