The layout issue is likely due to the significant changes between the latest version of Graphene, and version 1.9.4.2. The changes are more than cosmetic and goes down to the structural level, in order to support modern web features and compatibility with many different device form factors.
I would suggest to make a copy of the site, and perform the update on that copy. Any layout issues can then be addressed and fixed on the site’s copy, without affecting the live website. When everything is ready, you can then transfer the copy back into the live website.