Since the version 4.7.6, you can backup the customized html file as a ".bak" file, then it will be restored after an upgrade (in other word, the customized file won't be overwritten). For example, if you want to customize the file "webclient/login.html", you can modify the html content by yourself, and then just backup the file as "webclient/login.html.bak".
And here are the html files which support auto-restore:
/webclient/login.html
/webclient/main.html
/webclient/login_m.html
/webclient/main_m.html
/webclient/downloadpass.html
/webclient/weblink_update.html
/webclient/plugins/sendfiles/generate_weblinks.html