[arch-general] /lib to /usr/lib : custom kernel

[set]

Hello,

I updated one machine following instructions on archlinux.org and the process 
was flawless. That machine was running the Arch kernel.

I dare not do it on another machine running a custom kernel. Will a system 
update break the setup because /lib/modules contains a kernel not managed by 
pacman ? If so, how to proceed ? Should the custom kernel be removed first ?

Thank you.