If you click on a link to a site collection and get this error :

And then go to the SharePoint Admin Centre and still see it in the list, but clicking the link still give the 404 error above :

Then is means that the Home Page has been deleted. To get it back, go to any other site collection, then Site Contents.

Copy all the text in yellow below once in Site Contents :

Go to the site collection where you get the 404 error and paste it to the end of the link after the site name :

The page will display in the Site Contents screen. Go to the Recycle Bin :

Tick the box next to Home and then Restore :

The site is restored :

Be careful when deleting pages from the Site Pages library – don’t delete the Home page or it causes the above issue.