1. Your database will not understand Qlikview functions, so do not use them in SQL SELECT statements that are send to your database.
2. AutoNumber ([Column Three]) as (Column ThreeID) is not correct. Try square brackets: AutoNumber ([Column Three]) as [Column ThreeID]
3. Simply put an AutoNumber() around the if statement: AutoNumber(if(isnull ([Column two]),[Column one],[Column two])) as [Column Three]
I only put point 2. as a context sorry and did not put it exact correct syntax.
however 3. worked brill thank you
AutoNumber(if(isnull ([Column two]),[Column one],[Column two])) as [Column Three]
but I have found out if you do point 3 first then point 2, you can create the new field required (to help with the null entry's) and auto number field too.