I have just done this in a UAE installation of OS3.9 which I use for preparing stuff to copy to my A1200. I think I rebooted too soon after saving the file (I had just been editing it) and it disappeared. I don't know whether the same thing can happen using an OS4 filesystem.
I don't have an OS4 machine but I do have a copy of OS4 classic. Would that have a working startup-sequence on it which I could email to you?
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moto