Yes @szerendipal, when filtering the URLs in query edit mode, within PowerBI or Excel, select the option "contains" instead of "equals". This way all sub folders will be included.
I'm sorry, but what do you mean "filtering URL"? I'm not filtering anything, the table is empty. If I go to the query editor and click on Source setting there are no options you mention, it is just showing the link of the site which contains the folder and files - and which just don't show up.
@szerendipal Ah, I see. In that case I'm not sure what's wrong. Looking at your URL, it doesn't include sharepoint. My sites' URLs look like this:
https://tenantname.sharepoint.com/sites/sitename/ for example, where tenantname is the domain name that was registered when setting up office 365 (with the tenantname.onmicrosoft.com ending), not necessarily the one where the email's domain points to.
Hope this helps.
OK, thanks, I will email the support directly and leave a comment here once this gets confirmed. Until then, I will keep the topic open - maybe somebody else has something to add.