that happened to me once,.. and I can give two of the reasons

a) very long lines - for some reason if a line is too long mirc removes it

b) second reason (and this was using mirc v5.61) - there was a maximum file size you got to when editing in your editor, then you couldn't add any more text other than with notepad or some other editor..

Next time you go into that file with mirc it would crop the script at that max file size & you would lose code. I don't think that should be a prob in v6.16 though.