You're making a change that SQL Compare itself can't handle, as you're splitting a column and SQL Compare's script wouldn't have the knowledge to preserve your data.
There's good news and bad news.
The good news is that we can handle that via the addition of custom migration scripts. There's a video that describes how this works here:
http://www.red-gate.com/products/sql-de ... deployment
(it's the second one, called "A step by step guide through database deployment).
The bad news is that due to various implementation details this functionality doesn't work with SQL Azure. How often do you find yourself in situations where you need to add pre/post statements to your scripts? I think you'll have to carry on modifying SQL Compare's script manually for the time being, and hopefully we'll handle this in a later release.