You need to backup 2 setting groups:
1. Backup the INI file (HWiNFO32.INI or HWiNFO64.INI) containing general settings.
2. User preferences are stored in registry, under the following key: HKEY_CURRENT_USER\Software\HWiNFO32 or HKEY_CURRENT_USER\Software\HWiNFO64 respectively.
To backup these settings you need to run the "regedit" Windows tool, navigate to the respective keys and click Export. That will save them into a file, which after reinstalling the system can be launched to restore those values back.