If you rename the desc file in your local database for a package and try to rewrite the DB entry with --dbonly, alpm will still try to check for file conflicts, and then fail. This currently works as expected with 3.5.4 (without whining about "conflicting" files). I've had a bear of a time bisecting this due to a segfault that was introduced somewhere along the way when a local db file doesn't exist.

$ sudo mv /var/lib/pacman/local/filesystem-2011.08-1/desc{,~}
$ sudo pacman -S --dbonly filesystem
warning: filesystem-2011.08-1 is up to date -- reinstalling
resolving dependencies...
looking for inter-conflicts...
error: could not open file /var/lib/pacman/local/filesystem-2011.08-1/desc: No such file or directory

Targets (1): filesystem-2011.08-1

Total Download Size: 0.00 MiB
Total Installed Size: 0.06 MiB

Proceed with installation? [Y/n]
(1/1) checking package integrity [######################] 100%
(1/1) checking for file conflicts [######################] 100%
error: failed to commit transaction (conflicting files)
filesystem: /etc/arch-release exists in filesystem
filesystem: /etc/modprobe.d/usb-load-ehci-first.conf exists in filesystem
filesystem: /usr/local/share/man exists in filesystem
filesystem: /var/empty/.keep exists in filesystem
filesystem: /var/mail exists in filesystem
Errors occurred, no packages were upgraded.