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Since some users can get to the root folder of a sharepoint online site via "open with File Explorer" One of the users directly created a new folder in the root site(were the style library,Site Pages etc are) and then decided to move the following folders below to that new folder:-

Sharing links 
Site Asests 
Site CollectionDocuments
Style Library 
Transition Packages 
etc.. 
SitePages

Now when I load the homepage at SitePages/Home.aspx I get error and it doesn't load. Also of course the logo don't show and also when I go to the site content page the tiles of style library the sitepages and being shown and referenced from this new folder e.g

NewFolder/Sitepages
NewFolder/Style library

How can I fix this? I did try deleting the new folder but it says the files in in can't be deleted. When I moved the Sitepages back to the roor the icon doesn't show like the same in sharepoint deigner anymre as it use to.

Any ideas would be appreciated

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They are libraries. You need to re-create these libraries with same names in the site.

First, backup the original folders and files. Then, re-create the libraries with same names in the site. The content from the previous library could then be manually moved to the new one.

Some libraries are created by the site features, you can re-activate the features to re-add them.

For example: "Site Assets" library is created by "Wiki Page Home Page" site feature. "Site Collection Documents", "Content and Structure Reports", "Reusable Content" and "Site Collection Images" are added by publishing features. You can deactivate the features and re-activate them for re-creating libraries.

For the custom libraries, you need to re-create them manually.

Another method, re-create a site collection and move the contents.

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