As you know Microsoft Office Outlook Web App for Microsoft Exchange Server provides a rich Web-based environment for accessing a user's mailbox, including e-mail, calendar, contacts, and so on. Also, it provides way to customize features of Outlook Web App as well – you can customize the sign-in, sign-out pages, change the logo, font styles & colors and color of an element etc.
When you apply an update rollup package, the update process updates the Outlook Web App files if that is required. Say, any customizations to the Logon.aspx file or to other Outlook Web App files are overwritten, and you must re-create the Outlook Web App customizations in Logon.aspx.
As the best practice (and to avoid this scenario) I would ‘recommend’ before you apply any Exchange Server update rollup, make a backup copy of the customized Outlook Web App files; re-apply the backup files, if it’s needed.
- After patching, you can copy your customized files (after checking they don't cause any regressions) into the new version's folder which will also be in that OWA directory.
- Keep in mind the files you modified could always be changed in a new Service Pack or Roll-up.
- Don't just copy your old customized one into the new version directory and overwrite the newer file. I would recommend you to take the time to open up the new version and make sure things haven't changed, then copy/paste your changes back in.