Our general recommendation when upgrading CLC Genomics Server software is to upgrade in place.
Choosing to upgrade in place, that is, to install the new software to the same location as your existing CLC Genomics Server software allows your existing settings (e.g. File Locations, Users and Groups configurations, Import/Export directories, BLAST database, and so on) to be retained as these settings are stored under the installation area of the software.

When updating a CLC Genomics Server product, you will be prompted to specify whether you want to install to the same folder as your existing installation.
If you are not sure where you previously installed to and would like to check, then just choose to install to a new location. The old location will appear as the default, which you can then proceed to install to.

When upgrading to a new major version, you will also need to download your license again. This is described in the Genomics Server manual starting here: 
http://resources.qiagenbioinformatics.com/manuals/clcserver/current/admin/index.php?manual=Downloading_license.html