If I'm following your post correctly, you are taking the information from the Repeating Section and then creating a new Item in a different list or populated an Item in a different list, using that data. 

If your workflow is suddenly failing when certain fields are blank, I would first check the List that you're writing the data to and make sure that you don't have any columns set to "Required". If a column is set to required, and your workflow attempts to create an item where data is missing, it will fail. 

If that's not the case, then it would be helpful to take some screenshots or upload an export of your workflow that people can take a look at it to see if there are any errors in there. 

Hi Brandiwoodson,

I have come to a few situations with Nintex workflows not able to handle blanks, not specifically to deal with repeating section. 

The workaround I used is to add a 'runif' or a 'condition':

1) Package all action to parse RS, update field etc. into an action set.

2) Put the 'action set' under 'runif' or a 'condition' to skip all actions related to you this function of your workflow if the said field in the list is blank and  needs stay remain blank:

  =>  list field ({CurrentItem:yourField}) or output variable ({WorkflowVariable:varOutput})  = varBlank 

3) Please note the workflow doesn't allow having conditions or runifs with blanks, to workaround that, I create a text variable with no default value called 'varBlank' and use it in the condition to resolve

I am happy to answer any questions specific to your implementation

Regards,
Ashish