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I would use two separate projects. One would set up your base infra including the longer-running scripts that cause the problem. The next would set up the application-specific infra, including your DB migration. That allows you to put a health check in your deployment script or similar, between running the two projects.

This could all be done very easily inside an automation-api program too. Though if you're not already using that, I wouldn't start just because of this factor.