I still prefer upgrading through a cleen install and preserving my /home directory. However, I always have to pair my bluetooth devices after a fresh install. Where is the configuration stored so that I can just copy some files after a fresh install? I use the bluetooth indicator, but it does not seem to store the information on my devices in /home.
So it turns out the configuration is stored in /var/lib/bluetooth/aa:bb:cc:dd:ee:ff where aa:bb:cc:dd:ee:ff is the mac (I hope it is MAC) address of your device. To keep the configuration trough a fresh install, just backup and copy this directory over.
Thanks Bastien Nocera for the tip.