I tried upgrading from Mnemosyne 1 to Mnemosyne 2, but a large fraction of the cards were damaged in the translation (for example, I'd often made double-sided cards, then deleted one side, in Mnemosyne 1, but Mnemosyne 2 was not happy about this).

I occasionally deleted one half a of a double-sided card and I do not recall any odd behavior when I upgraded to 2.x... Have you tried exporting your cards with learning history and importing them to a 2.x installation? Or brought this up with Peter?