We ran the latest upgrade on Odoo9 website builder (using Clean theme) with the fresh code and after that the HTML customizations we had done prior to that were removed, e.g. we created a few pages and added them as links in the custom footer which is under Main layout. After the upgrade the custom footer was reverted to the default mode - the links were removed however the custom pages are still in the database.

Is it a bug? If it's as per design, could you tell us how to preserve customizations prior to running an upgrade?