@BregBF, it’s not uncommon for long time users of BigFix to create a folder specifically to store these mandatory files. For example, on my Windows-based root BES server in my lab there’s a folder named BES License located under the standard C:\Program Files (x86)\BigFix Enterprise path.
Additionally, it critical to securely store the PVK passphrase used by BESAdmin to unlock the installation for updates, etc. If your organization has an enterprise password management service like Secret Server or similar… please use that. Alternatively, I use LastPass to store the PVK passphrase, license.crt, license.pvk and masthead.afxm for all of my lab environments. Please do not rely on local copies and/or text files as these can fail at the worst possible timing.
I hope this is helpful.