There is a workaround, or it works for me at least. You need a layout slot other than your live layout that you don't mind overwriting.
1. Make your changes to war base and save
2. Select the war base slot, 'Copy' & choose the spare layout slot to paste the layout there.
That's it. Then, for me, logging out of the game and back in again doesn't lose the changes.
[Workaround inspired by Conqueror at UK Hit Squad - great alliance btw if anyone is looking for a good one!]