changing
CODE: SELECT ALL
well_known="$HOMEDIR/$user/web/$rdomain/public_html/.well-known"
to
CODE: SELECT ALL
well_known="$HOMEDIR/$user/web/$domain/public_html/.well-known"
in the file "v-add-letsencrypt-domain" solved the issue for me.
https://forum.vestacp.com/viewtopic.php?f=11&t=18593&p=77111&hilit=lets+encrypt#p77111