Finally, here's how I did to temporarily fix this bug.
edit or create /opt/retropie/runcommand-onstart.sh
add these lines
##reset bluetooth when launching mupen64,vice (fix controller cannot reconnect after get disconnected)
if [ "$1" == "c64" ] || [ "$1" == "n64" ] ; then
sudo hciconfig hci0 reset
fi
each time you launch a N64 or c64 game, you must reconnect (simply press ps button) the controller when game is started.
now if controller get disconnected or out of battery , you can reconnect without issue.
it also work if during the game a second controller want to connect, it is now recognized.
hope this help