No, perhaps I should have been more clear. I made the change but we didn't release it yet. I also made the history generation a little more efficient (but from what we know now, I think using SQL for the pointValues table is the problem). Also I did that in the 3.x stream.
I would personally restore your systems using a JSON backup into a new database and then migrating the data in. I see no problem using the existing database in place. I don't believe its pointValues table will be purged by the NoSQL module, so that will just linger, but to what detriment I couldn't specifically say. You could manually purge it yourself at the sql console, as well, and in time the database file may shrink.
Edit: You will probably need to email us about the license.