Default folders such as Desktop, Music, Documents, etc. listed as regular bookmark
My Music folder is now placed in the custom bookmark section of Nautilus after renaming my Music folder in $HOME to Music_ and a reboot, this was done in order to troubleshoot an issue. The Music folder also lost its music icon, after renaming it back to the original name "Music" and a reboot, the icon didn't reappear or moved back to the default home folders such as Home, Downloads, Music, Documents, Videos and Pictures. I also removed the bookmark of the Music folder from the custom bookmark section to see if it then gets restored to its original place, but no luck.
I had this a few times in the past as well, I couldn't find an easy solution back then either.
To give a more visual example of where this folder has been moved too, see the image below, which is just an example where the Documents folder would've been moved to the custom bookmark section.