As the names of the Workspaces are what Keyboard Maestro uses to recall the window there isn’t a “rename” as such. You can make an unlimited number of new ones and delete as many as you want but the window positions are linked to whatever name you originally gave the workspace.
The previous “rename” feature didn’t actually rename it replaced one of the 12 Workspaces with a new one.
But it’s a good point that you should be able to rename and keep the data. I will do that!
In the meantime you could Restore a Workspace, make a new Workspace name and resave each window to the new named Workspace. If I were you I’d keep the A,B,C ones for a couple of days and wait for the update.
This is what’s interesting about uploading a Macro - others will use it slightly differently to me. But that’s also what makes this an interesting thing to do. 
Thanks for being the Beta tester!