Synchronizing
Applying the differences, carefully.
Synchronizing generates the SQL that makes the Target match the Reference, shows it as an ordered list of steps, and runs them one at a time against the target.

The Script #
The steps are listed in the order they'll run, with each statement shown beside the list. The order comes from dependencies between objects, so tables are created before the foreign keys that reference them, and dropped in the opposite order. (Dependency analysis can be turned off in the setup, but there's rarely a reason to.)
The target and reference names are shown at the top of the view, which is the last place to notice they're the wrong way round. If you disagree with the script, go Back and change the options rather than running it and repairing the result.
Running It #
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Click Synchronize.
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Confirm the alert, which names the target database. Read that name.
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Watch the steps complete. The button becomes Cancel while running.
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When it finishes, the view reports that synchronization is complete.
Cancelling stops before the next step. Steps that already ran stay applied; there's no rollback across the script.
When a Step Fails #
The run stops on the failing step and shows its error. Choose Continue to run the remaining steps or Stop.
Think before continuing. Some failures are independent, such as an object already dropped by hand. Others cascade: if creating a table fails, every later step that references it fails too, burying the first error.
Recipes #
To synchronize safely
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Export the target first: structure only gives you something to compare against, and a full export gives you something to restore from.
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Run the comparison and read the results, especially Removed.
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Read the whole script. For a substantial change to production, copy it out and run it against a copy of the target first.
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Synchronize, then run the comparison again. A clean second comparison confirms it worked.
To use the script without running it here
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Copy the SQL out of the pane.
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Paste it into a migration file, or into the Query view to edit before running.
This suits changes that need code review or a deployment pipeline.