No. Typically not.
Usually nothing can stop the med board process besides a court-martial and even then, there are rules that have to be followed. There are so many scenarios that could be involved here that I cannot provide a more definitive answer without more information. A FLIPL may affect a person trying to outprocess, but it will not have any affect on the med board process.
You might want to consider anonymous call to JAG or the IG. They can provide specific information about your situation.
I hope you found this information useful