If an administrator wants to remove the customization made by TLDC there is no documentation for how he/she should do it and there is no script that counteracts the effects of tl-desktop-activate.sh.
What you actually have to do:
Remove the symlink /opt/thinlinc/etc/xstartup.d/35-tl-desktop-activate.sh and remove the symlinks in the user's home directories under ~/.config/menus/.
The script called tl-desktop-restore is actually not related to TLDC. This might also be confusing due to the name.
Related: Bug 1891
If we can solve bug 1891, then there's likely no need for this bug.