on the drive reveals that it is in fact in the same folder, but the library creates a new tree
I suspect you have incurred the "Capitalization" problem that is known to cause duplicate 'folders' in the Lightroom panel only.
Jim Wilde is the expert to answer these problems. The links have some of his posts- follow through his suggestions.
I think this is the right answer, but none of the suggestions I have found to correct it has worked - only generated errors. I may just have to rebuild the catalog again. Thanks for the direction!
If you would care to post a screen-clip of your Lr folder panel showing the 'duplicate' folders, we may be able to step you through the method to fix. (without the error messages)
Have you proved the 'duplicate' folders might have letters that differ upper/lower-case?
Hover the mouse cursor over a folder name for a pop-up of the full folder path and note the exact letter case.