The customized configuration.js file is overwritten under the path C:\Program Files\Citrix\Receiver Storefront\HTML5Client post Storefront upgrade
Backup the configuration.js before storefront upgrade.
Or, leverage web.config or default.ica for customizing HTML5.
It's the product install folder, so it's by design that the configuration.js will be overwritten post upgrade.
We can reproduce the same behavior by just upgrading HTML5 CWA.