Due to the numerous improvements and changes in the core framework of the product, the installation of Altaro VM Backup version 5.0 upwards creates a new settings profile and a new backup folder for a fresh start, however your old settings profile from 3.5 will not be removed.

As you can see below, both settings profiles will be kept in the "C:\ProgramData\Altaro\" folder:
 
The purpose of keeping the old settings profile is to facilitate the restore of backups taken with version 3.5

To restore backups taken with version 3.5, you may do so as follows:

1. Uninstall Altaro Hyper-V Backup version 5.0 from "Uninstall Programs" from Control Panel
2. Download the version 3.5 installation file from here.
3. Install version 3.5
4. Restore the VMs as required according to these steps
5. Uninstall Altaro Hyper-V Backup version 3.5 from "Uninstall Programs" from Control Panel
6. Install version 5.0 (Download from here if needed)
7. The settings of version 5.0 will be restored as you left them in Step 1 above
8. Continue backing up in  version 5.0 as usual