I believe all is well, but their website has become a bit glitchy.
I just transferred 25,000 "Baby Ultimate Rewards points" from my Freedom account, combining them with my balance of "Real Ultimate Rewards points" associated with an Ink card (both in my own name).
I logged onto Chase online, went to Ultimate Rewards. When I first tried to access the Freedom card, my browser kicked me out - the Chase online sign-in page reloaded, and I was not signed in. It did this about 4 times in a row. Finally, I was able to get in and access the freedom card. On the Freedom card page, there's a rounded light-blue rectangle near the upper right corner of the browser window (immediately left of the Search icon). Click the downward-pointing arrow to the right of your Points balance: you should see your Freedom card, with points balance, and all other UR-earning Chase cards in a dropdown list; at the bottom of that list, there's a link to "Combine Points". THAT is what you want. Click that, and it brings up a "Combine points" page with a two-column interface where you can choose the UR source ("Move my points from") on the left, and the destination ("Move my points to") on the right. Select one from each column and click Continue....you should then have the option to specify the number of points to move.
It worked just fine for me once it stopped logging me out.
So, I think all is well in UR-land. Give the above a try and see if it works.
Hope that helps (and I hope we can all sleep a little better now...I know I will).