Scrivener does not recognise projects after updating to El Capitan and having to re-register Scrivener

Scrivener does not recognise my projects after updating to El Capitan and having to re-register Scrivener to 2.8. If I open files via Spotlight, I get the following error message:

“There was a problem saving the project ‘Writing gigs.scriv’.
Not all recent edits could be saved. Files that could be recovered have been saved to … The project will now close.”