Hi Ryan, Thanks a lot for the very detailed report. Can you check in Settings -> Configure digiKam... -> Image Editor -> Versioning at the bottom in the "In main view" section, whether you have any of the "Always show..." options set? This could explain why some images are missing, but not why there is a discrepancy between thumbnail and table view. I assume that the case in the screenshot of just one image is only reproducible by moving images around outside of digikam? All in all it clearly sounds like an upstream issue. If you don't mind answering my questions, I will open the upstream bugtracker issues once we fleshed the problem out.
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