You don't want to import images into Lightroom and then use your operating system to move them to other folders. Doing so confuses Lightroom because it keeps track of your images based on where they were imported to or where they were moved to from within Lightroom. If you look at your folder tree in the Lightroom library module you will be of little identify the folders that are missing. Right click on the ones that are missing and choose the option to update the folder location. Then you will be able to show Lightroom where you moved those images.
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