This is because the script generated would contain a DROP TABLE statement. Of course it would have saved everything in a temp table before being dropped and re-created the table so nothing would have actually been lost.
Even still, it is probably a nice little safe guard for those who maybe aren't that used to SQL Server but I am so: how to get round it?
Solution
If you are confident that you are a legend with your SQL skills and you just want to be left alone you can disable this warning.Go Tools » Options...
Go Designers » Table and Database Designers and then uncheck "Prevent saving changes that require table re-creation"
Job done - enjoy at your peril!
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