A factory reset won't clear the option keys, they would be retained and unaffected. The only way to remove an option key is to use the API, this can be done either through the web interface under Configuration > API, or using SSH.
xCommand SystemUnit OptionKey Remove Type:
<DualDisplay, NaturalPresenter, PremiumResolution, MultiSite, RemoteMonitoring>
I did this the other day on a C40, I needed to remove the MultiSite option key, but using the above command didn't work as it kept giving me an error for some reason. So instead I had to remove all the option keys using the below command, and then had to add them all back using the web interface afterward. If you have to go this route, you'll need to lookup the option keys from Cisco's Licensing Portal > Get Other Licenses > TelePresence License to Resend.
xCommand SystemUnit OptionKey RemoveAll Confirm: <Yes>
