Lost modifier after update

Do you have numlock, or capslock, or scroll lock on?

– Thomas Adam

The keycodes don’t match. xev shows the keycode as 115:

keycode 115 (keysym 0xffeb, Super_L)

xmodmap -pm shows it as (0x7f), which converfted to decimal is keycode 127:

mod4 Super_L (0x7f), Hyper_L (0x80)

You may have multiple keyscodes that have Super_L assigned as their keysym.