You may need to replace not just char(13), but char(10) as well.
If that doesn't fix it, the characters that you are not seeing may be something else. Cast the column to varbinary and see what the characters are. For example, the following query (where I have appended AAAA to the end of the first line and to the beginning of the third line to make it easier on the eyes) shows that I have two pairs of 0D0A, i.e., char(13) and char(10).
DECLARE @x VARCHAR(256) =
SELECT CAST(@x AS VARBINARY(MAX));