It sounds like duplicate entries in the data-base?
If that's the case re-scanning should fix it (Settings->General 'Scan Again').
Just out of curiosity. Do you have duplicate files in the 'file explorer' as well or only in 'search mode'?
I am in the habit of making a backup of the Bank Presets folder every time I make significant changes to it. It might only be a few hundred megabytes extra, but the time spent on crafting banks is irreplaceable. if something goes wrong you can just dump everything and unzip your backup. Same goes for the Sessions folder. I don't like Dropbox, syncing has always been a mystery to me.