This may be of help:-
First of all as a back up make a new video folder and call it something other than the video folders you already have e.g. dabthoms videos - right-click on your video folder and copy to your new folder. Then....
Go into Libraries and open Videos
In the library pane, next to "Includes" it will probably say in blue "2/3 locations". Click on this
You will probably see 2/3 (one being the new folder you have just made) entries for where videos are stored - click on the one you want to be the default save location and delete the other one that is not the new back up folder.
See if your second copies disappear and then delete your new folder.