Core component of SQL Server for storing, processing, and securing data
Do I understand this correctly, that the files have data errors of various sorts that you correct in the target tables? And sometimes that these corrects are applied incorrectly?
It is difficult to explain a complex problem in a short and concise post, so there is a risk that important details get lost, and therefore I may be misunderstanding you. But from what you seem to say, my gut reaction is that you should have two sets of tables. The first set should mirror the source files exactly. Then you have your next set of tables which is your actual DWH which you query and make analyses from. To this you can add tracking table to track the manual changes.
I'm not much into the analytics space myself, but it's popular to talk about a medallion architecture with a bronze, silver and gold layer, where, as I understand it, bronze is the raw data, and gold is what you actually expose to the end users. Silver is then an intermediate layer to permit for stepwise refine ment.