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This is a bug that has been reported before. It often is caused by people resetting the sequence number for their photos in the camera to be 0001 for each photo shoot. If you're doing that then try turning off that feature.
Otherwise, the only workaround I know of is to copy the photos to your computer, using your operating system, and then bulk renaming the photos to some name that doesn't exist in your LR catalog, such as renaming DSC_0001.NEF to DSC_0001A.NEF
Thanks. I do not reset my numbering - thus unfortunately this doesn't solve the issue.
As you write - I may rename my pictures and import them like with a new name - however coming home with 4-5000 pictures after a wedding, it means you have to go through all pictures manually to identify the missing ones. I expected Lightroom to a an automatic tool.
I have not run into this issue but some people have indeed. Does unchecking "do not import suspected duplicates" help? Are these typically burst shots?