Impacts of changing lookup field

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We have a fairly large database in our Service Cloud site and are often required to migrate data to other sites. Up until this point, the Lookup field for our custom objects has always been left defaulted to "ID" so for migration, we would have to manually create the records in other sites since the IDs could potentially not match. To make this easier, we'd like to change the lookup field from ID to another custom field so that we can utilize the Data Import Wizard to import data to our other sites. Before we did this though, I was