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This is a fairly standard computer science question - there are many algorithms out there that are available to compare two data sets - I'm sure you've researched this so my answer is more about which service to use.
Given that the Lambda maximum runtime is a limitation, you might consider using Fargate.
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This is more like ETL use case. You could use AWS GLUE services. Glue can read and compare, which is fairly a query, and then it can process or populate additional column based on business requirement. Glue supports multiple framework and programming languages. Glue can read/write from multiple data sources including S3, rdbms, redshift etc. https://docs.aws.amazon.com/glue/latest/dg/what-is-glue.html
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