In recent versions of Linux, mouse natural scrolling setting is not persistent after reboot.
Edit X configuration for libinput
In file /usr/share/X11/xorg.conf.d/40-libinput.conf
there should be a block like the following:
Before
Section "InputClass"
Identifier "libinput pointer catchall"
MatchIsPointer "on"
MatchDevicePath "/dev/input/event*"
Driver "libinput"
EndSect
make sure to add Option "NaturalScrolling" "on"
After
Section "InputClass"
Identifier "libinput pointer catchall"
MatchIsPointer "on"
MatchDevicePath "/dev/input/event*"
Driver "libinput"
Option "NaturalScrolling" "on"
EndSect