Glad you found solutions
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Rlegro, one thing you obviously need to do before trying to delete duplicates again is to confirm whether there are actually multiple copies of the files or whether the same file is somehow being listed twice.This step seems like it should be unnecessary. Why would MB list the same file twice? Genuine question so I don't mean to sound obnoxious but I've personally never had this issue and it seems like something that shouldn't happen- a bug maybe?
Right click on a duplicate -> edit -> properties tab. Note the location on your disk.
Do the same for the other duplicate. Are the locations different or exactly the same?