Hi Jeroen,
When you upgrade from a FREE version to a commercial edition, you need to take care of the following:
1. Take a backup copy of your existing FREE version in a separate folder.
2. Unzip the commercial version and replace all the existing files.
3. Copy and replace the “store” folder from the backup copy.
4. Copy and replace data.xml and layout.xml from the backup copy.
The same steps apply when you upgrade to a new version.