The latest big update deletes some configuration files

A bit late reaction on this question… FYI…

>>> which checkupdates-with-aur 
/usr/bin/checkupdates-with-aur
~ 
>>> cat /usr/bin/checkupdates-with-aur
#!/bin/sh
checkupdates &
pacman -Qm | aur vercmp &
wait
~ 
>>> yay checkupdates-with-aur
1 aur/checkupdates-with-aur 1.0-1 (+5 0.49) (Installed)
    Helper script to check updates, including AUR updates
==> Packages to install (eg: 1 2 3, 1-3 or ^4)
==> 
 there is nothing to do
~ 
>>> 

:bird: