Updating the schema updates the definition of the dataset downstream that you intend to modify. This is done only in visual recipes and if ignored it might lead to inconsistencies in the flow.
In code recipes this is not shown, neither in scheduled jobs.
Thanks for your reply. I'm certainly finding the SQL recopies ask this every time. I just can't think of any scenario that I've not just clicked yes to update the schema. and I'm only suggesting that the first time this happens people get the option to ignore this in the future. I guess it is not a big deal - but I have many times clicked run on a big job - gone of for lunch and only to find it sitting there waiting for me to click update schema.