Serialize...
writer.Write(34); // change the version number by increasing it by 1. If it was 33, for example, change it to 34.
writer.Write(myBoolVariableOne);
writer.Write(myBoolVariableTwo);
writer.Write...// all of the other stuff that was here before...
Deserialize...
int version = reader.ReadInt(); // this will read 33 when you first load the server, but later after you save, it will read 34 because that is what you saved
switch( version )
{
case 34: // this is your new case
{
myBoolVariableOne = reader.ReadBool();
myBoolVariableTwo = reader.ReadBool();
goto case 33; // make sure you send it to the next (previously saved) case below
}
case 33:
...
}