If you are building your Flows from solutions and connecting to Common Data Service, you should use the CDS (current environment) connector.
When you do, if you populate lookup fields, you might get a “resource not found” error message.
If you get this error, like I did, you are probably just putting the guid of the record in the lookup field. You need to also include the entity name in your reference.
Once you do, your lookup field should populate properly. Thanks to David Yack and Antti Pajunen for this tip.