It would appear that you have two folders named "Lightroom Photos":
and that the one at the root of the drive should not exist.
Do I correctly understand this?
What happens if you select one of the pictures in the upper folder, right-click, "show in Finder"?
Are the upper photos really duplicated in the lower folders?
Thanks for comments.
Taking the 2015-05-25 folder as an example:
Earlier screen shot of "duplicate folder" shows 1 photo (a PSD)
The Main Folder shows shows 11 ( but does not include the PSD)
Show in Finder shows 15 photos including the PSD. The first _GPE files may be some temporary files, I do not recognise the naming. The other "extras files " would appear to be files I deleted from the Library within LR however I always select delete from disk to avoid orphaned files. The more I look at this the more I am concerned.
To find the files on the HDD not inside LR:
In the Library module first check 'Show Photos in Subfolders,' then click on your top-most Pictures folder and choose 'Synchronize Folder.' In the popup check the boxes 'Import new photos' and 'Show import dialog before importing.' This will show all the files on HDD that aren't currently imported into LR. It could take a few minutes for the Import module synchronization process to finish–Wait until it's completed. If you want to delete the image files click 'Import.' Once the files are imported you can 'Select All' (CTRL + A), create a new collection and move them all into it. This allows you to filter the Grid view focus on only those files and allow checking folder locations, etc.
Keep in mind that reimporting files inadvertently deleted outside LR will cause you to lose all edits done to those files! As long as you're sure you didn't delete files outside of LR you should be OK.
The folder structure is such that the top most, parent folder, holds all of the photos beneath it. So, in Lightroom you can correct your folder structure by rearranging it. You have a folder that says "Lightroom Photos" already and this should be your topmost folder. Click on and drag the 2014 folder into the Lightroom Photos folder. Then both folders in the 2014 folder will be part of the Lightroom Photos folder and will also show up in the 2014 folder. Do the same for 2015. You've already got this structure for the Photos folder below, as it and the other Lightroom folder contain the same number of photos (5,562). You can drag and drop folders as needed in LR to rearrange them as needed, but give it some thought first. It's ok to make a whole new folder if you are not sure, then drag and drop individual images into it by clicking on them and pulling them into the new folder. If a folder is then empty you can delete that folder, do this with care and after having your coffee, tea or cola in the morning, not after a hard day at work! Any changes you make to the folders within LR will be reflected in the folders on your hard drive. But, DO NOT do this from the hard drive as that will completely confuse LR. Rename folder names as needed before you move them to avoid confusion, for example, the second Lightroom folder, perhaps call it Other Photos. You can drag that whole folder, all 5,562 images, into the top most folder, too, if you want to. I think it works out best in the long term to have main folder that all other folders go into. See my folder structure below.