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Sounds like the issue might be within the dynamic input tool. Be sure to include the Database location under the input data source template / edit tab, and then under Modify SQL Query the 'Where Clause' should populate.
It's tough to say what is causing the Where Clause not to populate without having the workflow itself. A potential work around is to create a batch macro to update the where Clause with a list of dates that you would like to leverage. Note that this might take a bit longer and utilize more resources.
For Example, in the below I am updating the Customer ID in the Where Clause with the list of ID's I feed it from the Input tool.