Anyone have any experience overriding handling cost field on sales order? Have created a workflow but doesn’t seem to be sticking. The use case is handling fee is per customer so trying to source from a field on customer record. It seems like it loads the correct amount for a split second but then it goes back to $0.00

If you don't need manual adjustments and you always accept the value from the customer record, then it should work if you ensure your action is "before submit" or "after submit". If you need to make manual adjustments with such a solution in place you could add a condition to check for some sort of flag. Alternatively, test out every action trigger point. Maybe you'll find something that works better than before/after submit (depending on your workflow design (e.g., have it source after customer selection).

Yeah was thinking a before submit but their would be cases where handling fee will be set as $0 and not the customer defined value. Tried on entry, after field edit or sourcing on a few different fields and still no luck, seems like anytime the shipping method is updated it’s changed.

As I mentioned, with Before/After submit you could add a custom field to work as a flag (WF on / WF off condition) in instances where the workflow shouldn't run. It would require the end-user to select that flag (e.g., checkbox) if they want to save their input to their field.