The extra fields on the documents related to the fifth stage are not a problem as they can simply be ignored. You will need to update the "Form" fields on existing "in progress" documents to reflect the new form you've created, and you may need to make other field adjustments as well depending on your new workflow.
In other words, you should only need to create a single "cleanup agent" that will be run against all in progress documents which would modify (and if you like delete) all fields that have been impacted by this design change. It would contain code similar to this:
FIELD Form := "Newformname";
FIELD Stages := 1 : 2 : 3 : 4;
FIELD FifthStageStatus := @Deletefield;
FIELD CleanupFlag := "Yes";
SELECT Form = "Oldformname" & Status = "In progress";
Be VERY careful how you set up the agent. You could easily screw up older/completed documents that should not be touched if you don't know what you're doing. It might be safer to create a temporary "cleanup" view which selects only the documents needing cleanup, and set up the agent to run on "Selected Documents" instead of all documents in the database.
One technique that extends on this approach is to create the view such that documents that are being "cleaned" will remain in the view after the agent runs on them. You would do this by writing the selection formula something like this:
SELECT (Form = "Oldformname" & Status = "In progress") | CleanupFlag = "Yes"
You would then add columns to the view that show various fields that the agent is supposed to change, and an icon column that would display a red X or green check depending on whether that document had been cleaned or not. This is a great way to test the agent on single docs and see the results instantly displayed in the view.
Hope that is what you were looking for.