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Generate Change Script Challenges

This question was posted to the wrong forum, reposting here.

I had this working... lost my hard drive... re-installed and can't remember/find the fix.

Use Case:
Run generate change script.

Tables with Foreign Keys have an auto generated [ID] column appended at the end. For example, a table with five non identifying relationships has

integer [ID],
integer [ID],
integer [ID],
integer [ID],
integer [ID],
integer [ID]

At the bottom of the table. The change script fails and basically eats the database.

Run the change script a second time,

It works.

I can deal with this in a development environment where I can erase all the data when ever I feel like it, but for production the tool is basically useless.

There was some setting deep down in Settings that fixed this, I can't remember what it is. Can somebody help?