Sharepoint stop syncing with Onedrive for a specific site. Explorer shows folder that was previously synced using Onedrive, eg with cloud icon. Now it shows the Onedrive folder as a local folder.

After some Internet research. You can fix this by using the following steps:

1. Use your browser, connect to Onedrive, My Files
2. Delete all shortcuts. There is a linked icon next to the file name.
3. In your computer, if any orphaned folders were synced, but now missing the cloud icon, backup and delete them.
4. On systray, using the OneDrive app, check for the sync to finish. I let it run overnight.
5. Exit and launch Onedrive
6. On SharePoint, click on the sync button to add to Onedrive.
7. On Explorer, check for <org>/SharePoint folder etc This may take a few minutes.