Based on the information you have provided, it seems like the issue with your FusionAuth deployment is related to license registration. It's possible that the non-production license you were using is not appropriate for your current usage, and that may be the reason for the message you received.
Regarding your question, deactivating your non-prod license and activating your prod license should not affect your current configurations, users, and permissions. As per the documentation you shared, deactivating a license does not remove any configuration previously saved while the license was active. Therefore, if you activate a new license, all of your previous configurations and settings should still be in place and accessible.
It's always a good idea to take a backup of your current configuration before making any changes, just in case. Additionally, I recommend double-checking with the FusionAuth support team or your Client Service Operations Specialist to confirm that switching to the prod license is the right course of action for your situation.