The Grubhub tech blog put up an article about how they did exactly this when they moved both the legacy Seamless and Grubhub data to a new SOA platform while all three were in use: bytes.grubhub.com/a-migration-stor....
The short of it is, yes, you should have a separate service handle the migration, but also consider giving that service direct database access and ensure that all responses are idempotent in case communication fails in the middle of a migration.
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The Grubhub tech blog put up an article about how they did exactly this when they moved both the legacy Seamless and Grubhub data to a new SOA platform while all three were in use: bytes.grubhub.com/a-migration-stor....
The short of it is, yes, you should have a separate service handle the migration, but also consider giving that service direct database access and ensure that all responses are idempotent in case communication fails in the middle of a migration.