All the important information is contained in two places:
The BES Client folder (and subfolders), which are by default at: “C:\Program Files\BigFix Enterprise\BES Client”
The registry key “HKLM\Software\BigFix\EnterpriseClient” and subkeys.
If you export and import the registry keys nightly make sure the agent is stopped and isn’t restarted (stop the agent before you export and start the agent after you import).