I have been using
["AmmoboxInit",[_ammoBox, false,{true}]] call BIS_fnc_arsenal;
to initialize the arsenal empty. However, if I re-run this command, it will not re-empty the arsenal.
I could use BIS_fnc_removeVirtual*Cargo
to remove each item there, but is there a way that allows me to remove everything from it?
You can clear the Virtual Cargo using this line
_ammoBox setvariable ["bis_addVirtualWeaponCargo_cargo",nil,_true];
This will remove everything you added using the BIS_fnc_addVirtual*Cargo calls. So that should make your Arsenal empty.
Or optionally you could completly remove the Arsenal using:
["AmmoboxExit",_ammoBox] call bis_fnc_arsenal;
and then re-add it again.