I was set to ‘custom scanning’. Is this a new setting?
I have set it to ‘media store’, but in changing that setting all is rebuild. Which with 46000+ photo’s takes more than a day. And I still had the same issue.

When having it set to not autosave, I believe images disappeared after saving. However now trying to reproduce to be exact in my answer I do not see this behaviour. Scanning type is set to ‘custom scanning’ now.

The folder does show, but with 0 images and folder thumbnail becomes blank.

Thanks for the quick response!