@myki,
Just another thought ... do you have any of the Kobo hacks installed? If so, it might be an idea to uninstall them and see if you can get a 'pure' H2O working reliably with calibre for a few days before retrying the hacks - one at a time.
The only reason I ask is because I also have had the calibre/malformed database scenario. Both times it was within a couple of days after I'd installed a hack. The first time it was after installing KOReader on an AuraHD (many months ago). The second time was last week after installing the NightMode hack on my H2O. I really don't understand why I had these problems as Kobo owners seem to have installed these hacks with no problems whatsoever. As I was only dabbling for my own amusement, I decided not to pursue the problems and have had no further malformed database problems.
Note: I've never had any problems at all with the Kobo Patcher hacks. I definitely wouldn't want to be without those
