If you have an old clone made from before the transition and try to update it, I'm not sure what it says, since I don't have any of those around any more. It has, after all, been three years since Fossil began to move on this problem, so that it's largely a past issue for us now.
This transition time was indeed annoying for us over in Fossil land, but Git's going to have to go through a transition like this, too. The question isn't whether but how long we'll have to wait for it to begin and how long it'll take to complete.