Windows share shows file folders command line can't see and Sonarr points to those folders

So yesterday I redid my file folder structure and along the way I screwed something up. It used to be /Downloads right in root and I changed it to be 1 folder "data" and then have my media under it so it's /data/Downloads or /data/PlexMedia. I deleted the folders in root I didn't need however they are still there on windows file share.

https://i.imgur.com/npQ8rQy.png

on command line logged in as root they are not

I am new to Linux but I do not understand how folders cannot be see by root command line. On the windows share I do not have the option to delete the folders even when I gave my user accound sudo permissions.

Additionally I'm having an issue with Sonarr where it points to my root directory even after deleting the container + volume and reinstalling. A copy of the docker compose is here (0bin_5xV4BNBI.txt). This is my container volume mapping which is to /data NOT the root directory

the relevant sonarr image:

I've tried the Sonarr discord for help and they told me it was and OMV issue.

I figured out the issue, when I removed Downloads, Music, Photos, PlexMedia from Services/Shares those folders stopped appearing at the top level.

My confusion that Sonarr was somehow adding the root directory and creating these folders was due to folder permissions issues.

I'm still a bit confused by Services/Shares and Storage/SharedFolders but atleast things are as expected.