I assume you're not actually doing this in Power Automate Desktop, but are instead using cloud flows. This forum is intended for desktop flow questions only. The correct forum for questions on cloud flows is here: https://powerusers.microsoft.com/t5/Building-Flows/bd-p/BuildingFlows
As to your question, you will likely need to have a way of mapping files in the source directory and the destination directory. Might make sense to have a separate table where you map an item/file Id from the source directory to the item/file Id in the destination directory. You should have the first part of your flow (the one that copies the file when the status is "Final") populate this table. And then you would be able to use this table in your second part of your flow - to check if a matching file exists and then to delete it. You should also make the flow remove the entry from the table when the file is deleted.
You can use a separate SharePoint list or a Dataverse table to implement this mapping. Otherwise, you can use a SQL database or even an Excel file to do it.
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