I have a symbolic link from ~/Documents to ~/Dropbox/MyDocuments.
However I noticed that Catalina from time to time deletes my symbolic link and replaces it with a new Documents folder. I think its happening at a reboot but may happen at other times as well. Any way to prevent this?
Open door but before we skip over the obvious…
Check if DropBox has the permissions in System Preferences > Security & Privacy ?-)
Are you sure it’s not Dropbox that’s doing it?
"As of mid-2019, Dropbox no longer follows items outside of your Dropbox account that are linked to by a symlink.“
See more:
I don’t think that should be a problem? If I’m reading it correctly the OP is creating a symlink outside his Dropbox directory pointing to a directory inside his Dropbox directory and not the other way around. Dropbox shouldn’t care (or even know) if there are symlinks pointing at files or directories inside the Dropbox directory. (~/Documents->~/Dropbox/Documents, not ~/Dropbox/Documents->~/Documents)
What I’d try is deleting the symlink and leaving your home directory without a Documents directory for a bit. If one shows up (like after a reboot) then you know it’s Catalina doing it. Catalina is pretty fussy about Desktop, Downloads, and Documents.
That’s not how I read it.
From the original post:
I read that as meaning that the link had been made like this:
ln -s ~/Documents/ ~/Dropbox/MyDocuments/
in which case Dropbox would definitely see that MyDocuments was a link.
I suspect that macOS would not like it at all if you delete the ~/Documents/ folder and tried to link from ~/Dropbox/MyDocuments/ to ~/Documents/.
Now we’ll have to wait to find out which of us read it the right way! In person, this would be the sort of thing over which drinks ought to be wagered, largely because when one wagers drinks, there really are no losers 
I’m creating a link outside of the Dropbox (/Users/scott/Documents) to a folder inside my Dropbox folder (/Users/scott/Dropbox/MyDocuments).
I thought it’s a Catalina issue because I haven’t seen this issue before. One suggestion I had was to use the Get Info and mark the symbolic link as locked. Going to see if that helps.