I think you have changed something by mistake in the function init script that compiles the CfgFunctions. Basically there is no compileFinal in there anymore. This means the extra security added by this is now gone.
Basically an attacker can now re-compile everything.
bis_fnc_mp = 0;
initFunctions.sqf line 295
^ this will always return true!
Isn't it because you tried it in the editor? Because missionNamespace functions can be recompiled freely there for debugging purposes.
Yes, it was tried in the editor. Does that make a difference? If so, it should be mentioned here:
https://community.bistudio.com/wiki/Functions_Library_(Arma_3)#Adding_a_Function
It is mentioned there:
As a security measure, functions are by default protected against rewriting during the mission. This restriction does not apply in missions previewed from the editor...
https://community.bistudio.com/wiki/Functions_Library_%28Arma_3%29#Recompiling
But it probably deserves more attention, I'll find a way how to highlight it.