Nested content directories are when you have a folder selected as a content directory and also a sub-folder of that folder selected. What you could try is merging them into one (e.g. the My Library one), for Windows taking everything out of the sub-folder and placing it in the one you are keeping; Windows will ask if you want to merge and you say yes, then make sure that you remove the no-longer-needed folders from the list of cotnent diectories. You do need to be aware that if a scene or preset was saved pointing to one of the nested content folders its paths may include the sub-folder, which will then cause an error on the clean installation - that can be fixed with a text editor but it is a potential issue to be aware of.