i've had it happen to me before, so i just make a back up copy of my mirc.ini and remote.ini every time i make a major change just incase.
The thing about mirc only supporting a certian number of bytes was from pre-version 6, possibly before that even, where the mirc editor would only display a certian amount of data before cutting off the rest, so if you clicked OK, it would save to the file minus the data the editor cut off.