How to deal with--errors occurred, no packages were upgraded

Question

This has only occurred to me once before, I think.
I was running a pacman -Syu today and it was trying to upgrade kernel2612-cko2-swsusp2 with the new kernel26cko package. The old cko was installed by grabbing the pkgbuild, making and then installing. Pacman automatically picked up that there was a new version to supercede it.
Yet, I get a ton of "exists in filesystem" errors, which ends with "errors occurred, no packages were upgraded."
Now, I've been searching about the best way to deal with such situations. The common approach from previous posts is to force it, with the -f argument. Typically, there is a clause though, that you should only force when the files are owned by a package that pacman knows of. That is, if pacman -Qo [file] doesn't return anything, you are safe to force.
But, in this instance, the offending files are owned, and pacman knows about it. So, what's the way forward? Removing the old package manually? Manually re/moving the conflicting files?
Cheers

Answer 1

i think there may be a problem in the sane package from testing. i installed smaller chunks of kde (kde-common, kdebase, kdeadmin, etc.) and they all went fine, but when i tried to install kdegraphics, it gave me the error
[root@arch jerry]# pacman -S kdegraphics
Targets: libungif-4.1.3-2 imlib-1.9.15-2 libgphoto2-2.1.6-2 libieee1284-0.2.10-2
sane-1.0.16-2 fribidi-0.10.5-2 gimp-print-4.2.7-3 ghostscript-7.07.1-5
t1lib-5.1.0-1 kdegraphics-3.4.2-3
Total Package Size: 23.6 MB
Proceed with upgrade? [Y/n]
checking package integrity... done.
loading package data... done.
checking for file conflicts...
error: the following file conflicts were found:
sane: /usr/var: exists in filesystem
errors occurred, no packages were upgraded.
should this be filed as a bug report? i did a fresh install and did not have kde installed to begin with, but im pretty sure this happened also when trying to upgrade