I kept two notes below the file explorer (left sidebar) for sometime. When I moved them back into the usual notes section a “visible gap” appeared below the left sidebar that you cannot get rid of: The lelft folder pane can no longer be resized to full height.
Nothing changes with close/open obsidian. The only way problem disappears is if I copy/paste all notes + folders (except the .obsidian folder) and open the new location as a new vault.