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answers:

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How can I copy records from two Database, "db1.db" and "db2.db" with different column structure?

A: 

This will have to be done a table at a time, not a database at the time.

Since you mention the schema is different between source and destination, you will have to normalize this before making a copy. Most automated tools you might use will probably require the same schema to automate this process, or require you to map source columns to destination columns.

Chris Ballance