Safely point Joplin to my WebDAV location

I use Box drive WebDAV to store and sync my Joplin notes. I've this setup on one machine and want to replicate this another machine and both of them should point to the same shared WebDAV location at the end. When we install Joplin it creates a default storage location on the machine and on my new machine I change the location to existing Box WebDAV location. With this, I see the notes tree structure is completely messed up and only few notes are visible on my new machine.

Can anyone tell me what exact steps I need to do after installing Joplin to point it to existing WebDAV/ cloud storage location?