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How about Formatting the card after you get images off it. Seems like the logical thing to do. It is for me.
Are you renaming the images on import? If so, LR may not know those images have been imported.
I usually do that on my cameras.
Not so easy on the iPhone.
I still think there is a bug in Lightroom that needs some attention.
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No. I do not rename.
I do add GPS data as a matter of course.
That maybe the problem, I wonder?
That's a possibility since the meta data is different. I don't typically add gps until later if at all. Try it without the gps data and see what happens.