I ran into the same issue, it was caused by some attributes in the .json which are no longer needed in Atlas 3.
I solved it by removing the "pageTemplates", "cssFiles" and "designProperties" attributes.
So starting your .json at Widget level.
Hi Tedros,
If I understand you updated everything in Studio Pro. Have you also tried opening the app in the online Studio? Some things like Branding are easier to update/fix there. Maybe opening the app in Studio will fix it? Hope this helps!