By default, I'll definitely remove the removed stuff and update to the new.
I was thinking about adding a check box to revert to first editions. I like the whitelist idea, but I don't have a section for it yet, and it seems strange to add one just for these changes. I would like to allow whitelisting individual cards, or completely reverting easily, so I'll have to think about it some more.
I am, however, on vacation this week, so I won't be able to start updating until next week.