When manually entering in an alert through the web GUI, there does not appear to be a limit to the length of the note, which is nice (other than the field is very small in the web GUI). However, when you are adding a note to an open alert using the email reply method, Alert Central only takes the first 60 characters of the note. I don't know if this is a bug, or by design. Either way, I would request that it not be truncated to the first 60 characters, and allow users to enter in as long a note as they want.
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