To input data into a running workflow, you'd need to convert it into an Analytic App. To input data in the middle of a running workflow (vs at the start), you'd need to have a Chained Analytic App.
With that said, in your case, it appears you need to enter various pieces of information per row based on the incoming spreadsheet. Typically an Analytic App's interface is for standard / expected inputs. It seems like you basically need a spreadsheet with those missing value rows to be able to complete the dataset. Is there a reason you can't update the spreadsheet before executing the workflow to process it?
If it must be done during the run of the workflow, I'd go with the Chained App idea where the first app writes an output file with the rows that need data entry. Then the 2nd app will allow the user to input the path to a completed data entry Excel file, and uses that with the original data file (for those rows that were already complete) for the rest of the processing.
