When using a Merged Application, the backup preferences are stored in an XML file inside of the application package, for example, at the following location:

Windows:
...\My Merged Server\Server Database\Preferences\Backup\Backup.xml

Mac:
.../My Merged Server.app/Contents/Server Database/Preferences/Backup/Backup.xml

It is therefore very posible that this file may get overwritten when upgrading the application if extra steps are not taken.

Luckily, there are some built in commands that help with this. Here is an apporach for preserving this file during the upgrade.

1. Instead of overwriting the existing application with a new one, it would be better to use the SET UPDATE FOLDER command.
2. Then use the COPY DOCUMENT command to copy the existing backup.xml preference file from the currently running application to the correct location in the folder hierarchy set in step 1.
3. Then call the RESTART 4D command to have 4D restart itself and apply the update.

In this way, the backup.xml preference file becomes part of the update.

If a custom installer is currently being used to install and update the application, then the installer softare likely has an option to preserve the file or run a command that would help you to preserve backup.xml file.