This option never 'takes' or 'stays' for the next import and I don't see anything related in preferences. I think I can only ask if there is a way or if there will be a way in the future. Now, with the new mirrorless cameras and hefty megapixels and large file sizes, the CF cards are a boon to handling these images for capture and then to upload to Lightroom folders. Would love to not have to remember to 'include sub-folders' as nothing will show from the inserted card until that box is found and checked when importing into Lightroom...
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