WinUAE is said to repair the damage automatically when it detects the drive on WinXP. I never tried it.
You should load startup-sequence into Wordpad (WRITE.EXE). Notepad does not recognise the line breaks correctly. And before you save the changes you have to add a comment sign (semicolon) to the end of each line because Wordpad adds an additional carriage return character to the line breaks which AmigaDOS does not understand.
Bye,
Thomas