Se intendi il menù di wine basta che purgi il tutto.
Se intendi i menù dei programmi wine allora devi ripulire
in queste cartelle

$HOME/.config/menus/applications-merged/wine-Pr*
$HOME/.local/share/desktop-directories/wine*
$HOME/.local/share/applications/wine*
$HOME/.local/share/applications/wine/Programmi/