This nice fix was found here
add following lines in your ~/.muttrc
set duplicate_threads = yes
set move = yes
macro index M “T.*\n;WN” “Mark all messages as read”
start mutt, all duplicate messages will be marked as ~=
type T to tag message match ~=, then type d to delete. that’s simple nice way!!
highlight emails, right click the mouse,select Remove duplicate messages.
it’s amazing and simple.