I got myself in a bind where the repository was moved before I could make a change on the server. All I got was an error on my VisualSVN Server Manager that said "Can't open directory ..."
My solution, after trying those already provided, which did not work in my case, was to access the registry and modify the RepositoriesRoot entry to the correct path under
"HKEY_LOCAL_MACHINE/SOFTWARE/Wow6432Node/VisualSVN/VisualSVN Server"
This may be under the "HKEY_LOCAL_MACHINE/SOFTWARE/VisualSVN/VisualSVN Server" location if you're not running a 64 bit OS
Changing the value in that location got me back up and running.
... A little more detail as to why the other solutions didn't work:
1. I couldn't uninstall and then re-install because the uninstall attempted to access the original source location, which no longer existed.
2. Because of the state of my server I wasn't able to perform access the "Properties" menu option.