We were having this issue on a machine and discovered that the Start Menu folder with all of the RemoteApp Shortcuts had not been deleted when they removed the connections. We manually deleted these folders and we were able to restore the connections.
The RemoteApp shortcuts will be in a folder under:
C:\Users\%username%\AppData\Roaming\Microsoft\Windows\Start Menu\Programs
This has been kicking my tail for a few days right after I decided it was a great idea to use redirected folders.
Many thanks for this - finally got these profiles straightened out!