I have tried upgrading my Bitnami version from 3.0.1.8 to 3.1.2 and it worked without loosing any case data.
Amos is right about the manual installation, but if you still want to keep going with the Bitnami version I would suggest the following steps:
1. Backup your MySQL database for 3.0.1.7 version
2. Install the new Bitnami version of ProcessMaker.
3. Restore the backed up database in your new MySQL database.
4. Open your terminal and migrate to the installation directory, which should be [b] <Installation-Directory>/apps/processmaker/htdocs[/b]
5. Run [b]./processmaker upgrade[/b] for Linux system or [b]processmaker.bat upgrade[/b] for Windows
6. Restart the Apache.
I hope this helps. I would recommend you to perform a backup your old Bitnami installation before beginning with the upgrade. To take the backup of your Bitnami installation simply create a zip of your Bitnami folder and create a dump of the MySQL database.