The problem was caused because the system was using the nathan rennie-waldock PPA for xmbc instead of the team xbmc one which is now the official one.
I backed up the .xbmc
folder in /home
and let the update run.
After performing this partial update caused xbmc to be removed. I changed by PPA for xbmc to the official one and tried to reinstall to 13.1 (Gotham). However the xbmc-bin has been left kicking (note it was in the upgrade section, not remove in the original question) around so I first had to sudo apt-get remve xbmc-bin
. Once done I could reinstall xbmc from the official PPA. My user data was preserved.1
1 Note - I store my db into a mysql database, so YMMV. Additionally, this database had been upgraded to Gotham via another xbmc on the network. I'm not 100% sure this all would have worked without that being done prior.