User 2 tables/forms. One lets say called "Uploads" where you keep updating the current record and a separate table lets say "Upload_History" where you add a record every time someone submits a form. This way you can keep a single record with the combined data and history of every upload.
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that's one way to record form history, thank you for sharing your ideas!

I still wonder if the file someone uploaded in form A in a previous workflow assignment is deleted or not if someone remove or replace it when they edit form A in a later workflow assignment. There's actually an option for user to choose whether to "Delete the Actual file..." so I'm assuming if the form designer does not explicitly choose to delete file, then the files are still somewhere in the database.

If the file is not deleted, it would be great if we can still access it somehow. In your method, since we have original form and will create a new record of the second form whenever user create or edit the original form, we are cloning all files in every time user update original form. In my case, because the form can be updated 4-8 times in the workflow, if user upload 1 file when they create the form, it will be cloned 4-8 times when the flow finishes.