I am on ArchLinux and tried to upgrade from linux-zen 4.5.4 to linux-zen 4.6.2 once, and found out that all my gnome settings were gone. I thought it was just because my computer crashed or something similar. Due to issues with PSR, I went back to 4.5.4 anyway and resetup everything again.

Today, I gave it another try and went from linux-zen 4.5.4 to linux 4.6.2 (so the default kernel, not zen version). I found out that my /etc/pacman.conf file was totally corrupted and had random characters, it was unreadable. I then rebooted to linux-zen 4.5.4, and updated it to 4.6.2. Now, my gnome settings have all disappeared again.

I have also noticed that the files from various packages were corrupted, had to reinstall them. I guess there are probably more files that I didn't find out about yet.

I am using F2FS, and in all these cases I have switch to 4.6.2 it did a fsck on start and a lot of errors/warnings were printed that I have never seen before when doing a kernel upgrade. I guess that this is when my files became corrupted.
I am not sure what to do now, I guess I may switch back to ext4 to prevent this from happening again.