The intention is that the new client will refuse to run until you have reindexed the blockchain by running it with the -reindex command line option.
In Linux that's easy:
  $ clam-qt -reindex
In Windows, I'm not sure - in XP (the last Windows I used before kicking that dirty habit) you had to right-click, create shortcut, right-click the shortcut, edit the target, add " -reindex" to it, then apply, and OK. Or something like that. I expect it isn't so easy any more, with years of "improvements". Maybe someone who didn't detox yet can confirm?