I've had similar problems with exporting artboards that contain smart objects, when the smart object has a transform applied to it. In my case the smart object completely moved and changed size in the exported image. I had to flatten the document first, just like you did. I suspect there is a bug with transformed smart objects.
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Yes it look like there is a problem with resize and smart object transform
I explored deeper and open a new thred with a more precise and narrow description
We have the same issue. To us it is a very big deal as this basically makes use of smart objects in artboards impossible if you need to export those in different sizes.
I wonder how Adobe can ignore this issue.
This like screws the whole Export feature to be obsolete for MANY people.