Data shuttle replace workflows only adding or deleting every hour, not both


For some reason last night, for all of my replace data shuttle workflows (all run hourly), they have started either only deleting the applicable rows or only adding the applicable rows. Prior to today, each run would delete the rows then add the new ones, but now it does only one or the other.

The workflows are set to update in scope clients from a list of 1000 posted in Excel on SharePoint, based on a certain criteria in one field of the Excel sheet. Usually, the results show that @ 435 rows were deleted and @435 rows were added each run. Now, one run deletes the rows and an hour later another run adds the rows. So for an hour, every other hour, the reports / dashboard on that sheet are blank!

This has been running correctly for 6 months, all runs yesterday worked fine. It started with the run at 1am ET today.

Any idea how to resolve this?