From my experience for this scenario, I would clear all records in the data extension before doing the import activity. Hence you can start a fresh import.
You can clear records in the DE using Script activity with WSProxy like this:
<script runat="server">
Platform.Load("core", "1.1.1");
var prox = new Script.Util.WSProxy();
var customerKey = "Your DE cust key";
var action = "ClearData"
var result = prox.performItem('DataExtension', {"CustomerKey": customerKey}, action);
</script>
The thing I love in this way is that it will work even if the DE has a non nullable column.
And then put the script activity before the import activity in an automation
For example:
