For MP, you need to run the fnc_deleteSave on each client (saves are local) if you want to reset everything for all players.

waitUntil {!isNil "rvg_saveFile"};
if (call rvg_fnc_indexSaveFile > -1) then {
call fnc_deleteSave
};

You'll probably need another condition evaluation to make sure you are only deleting saves when needed, like a variable with the current version of the mission file.