I found the solution which worked for me. This Adobe help article explains the steps, which are as follows (added in case the link goes down):

1. After backing up your catalog, relaunch Lightroom.

2. Connect the hard drive (MyBook) that is repeating twice.

Note:

In this article, the labels—MyBook, Temp, Fred, and Mary—have been used as representative names to explain the solution steps in a clear manner.

MyBook denotes the hard drive that is appearing twice in Lightroom's Folders panel. Temp denotes another temporary drive that is required to resolve the issue. Fred and Mary denote the dummy folders created in Temp drive to resolve the issue.

3. In the Folders panel (Library module), click to expand both the instances of MyBook. After expanding both the drives, make a note of all the top-level/parents folders appearing under each drive.

4. Without disconnecting the Mybook drive, connect another hard drive (Temp) with your computer.

5. Using the File Explorer (Win) or Finder (Mac), navigate to Temp hard drive folder on your computer.

In Temp hard drive, create new empty folders corresponding to each of the top-level/parent folders that you noted in Step 3.

For example:

If there five top-level/parent folders appearing under the first instance of Mybook in Lightroom, create five new empty folders in Temp hard drive. You can name them as Fred1, Fred2, ..., Fred5.

Similarly, if there five top-level/parent folders appearing under the second instance of Mybook in Lightroom, create five new empty folders in Temp hard drive. You can name them as Mary1, Mary2, ..., Mary5.

6. Now, go back to the Folders panel in Lightroom.

Under the first instance of Mybook, do the following for each of the top-level/parent folder:

• Right-click (Win) or Control-click (Mac) a top-level/parent folder and select Update Folder Location from the context menu.
• In the dialog box that appears, navigate to Temp hard drive location and choose a corresponding Fred folder that you created in Step 5.

Similarly, under the second instance of Mybook, do the following for each of the top-level/parent folder:

• Right-click (Win) or Control-click (Mac) a top-level/parent folder and select Update Folder Location from the context menu.
• In the dialog box that appears, navigate to Temp hard drive location and choose a corresponding Mary folder that you created in Step 5.

Note:

At this point, both the instances of Mybook drive should disappear and the Fred and Mary folders should appear under Temp drive in the Folders panel.

7. Now, update the location of each of the Fred and Mary folders appearing under Temp hard drive to their original folder locations in MyBook drive.

Under Temp drive in the Folders panel, do the following for each of the Fred and Mary folders:

• Right-click (Win) or Control-click (Mac) the folder and select Update Folder Location from the context menu.
• In the dialog box that appears, navigate to MyBook hard drive location and choose the original folder (noted in Step 3) corresponding to the Fred/Mary folder.

Note:

If you get a message that the folder is already in Lightroom, select Merge.

You should now have all the original top-level/parent folders restored under one MyBook drive.

I just plugged in a portable hard drive and created one new folder for each of the two duplicate drives showing in my Library. You don't have to make them for any subfolders.
Then when you point it to the newly inserted drive the version of the duplicated disappears without actually moving any pictures. The same with the second duplicated version.

Then when you take your newly created drive and point them back to the actual storage location of the photos in Finder it loads them all to the same drive and includes all the original subfolders that were there. I tested by importing new files to a new folder afterward and it is working correctly again.