Same symptoms like Jerzy Luszawski @dr-agon wrote, except my links
pointing on:

/etc/ld.so.conf.d/i386-linux-gnu_GL.conf -> 
/etc/alternatives/i386-linux-gnu_gl_conf
/etc/ld.so.conf.d/x86_64-linux-gnu_EGL.conf -> 
/etc/alternatives/x86_64-linux-gnu_egl_conf
/etc/ld.so.conf.d/x86_64-linux-gnu_GL.conf -> 
/etc/alternatives/x86_64-linux-gnu_gl_conf

alternatives are also symlinks, pointing to real files
/etc/alternatives/i386-linux-gnu_gl_conf -> 
/usr/lib/i386-linux-gnu/mesa/ld.so.conf
/etc/alternatives/x86_64-linux-gnu_egl_conf -> 
/usr/lib/x86_64-linux-gnu/mesa-egl/ld.so.conf
/etc/alternatives/x86_64-linux-gnu_gl_conf -> 
/usr/lib/x86_64-linux-gnu/mesa/ld.so.conf

When I copied real files into /etc/ld.so.conf.d/ the problem is gone.
`update-initramfs -u` didn't write any waning anymore.

Update-initramfs seems to have problems with symlinks (why?).

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https://bugs.launchpad.net/bugs/1800719

Title:
  missing conf files noted on apt upgrade after distribution upgrade

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