Ok, so I have reuploaded the data to ArcGIS Online and retried the query, but it seems I have hit another issue, one which I have not been able to find any info on.
The following error is occurring when I either attempt to apply a query or a definition expression to the Scene layer. Weirdly, I can identify the features within a Scene layer i.e. if I click on the map, I get a popup showing the feature attributes.
Logger.js:5 [esri.views.3d.layers.i3s.I3SBinaryReader] Invalid attribute buffer size expected: 7676922352, actual: 25)
Does anyone know what could be causing these errors?