There’s a few good reasons this could be happening and a few bad reasons. 

Let’s start with the basics: 

1. Are you doing a ‘new’ data load or are you using the ‘data refresh’ function (this function is only available on enterprise licenses so you may not see it)
   1. New load in some cases can reset data and do a full shape rebuild. 
   2. You may want to try pasting the data into the existing data set. 
2. Have the column names on the ‘refreshed’ data changed?
   1. This could unlink the conditional formating from the shapes and thus clear the effect of your rules. 
   2. What steps do you have to take to restore your conditional formatting after it has been cleared?
3. Has this worked for you before and is only now not working?

With a little more information we can try to get you the right answer. 

Thank you for your support, Paul!

1. I am selecting Import data again to reload the data, I do not see a data refresh option although under Data Linking there is a bullet point that says Refresh your data source to see live updates although there is no option to just refresh, only import data.
2. Column names on the refreshed data did not change. I selected “Import data” on the Org Chart Shapes panel and it moves all conditional formatting settings to “Not applied to selected shapes.” Is it possible to add to a list of requested enhancements that when selecting the box to select multiple conditional formatting settings to “Apply to all” that it applies to all selections? Right now when selecting multiple, it only applies the change to one at a time.
   1. When importing the data from the Data panel, it seems to have different functionality than from any of the other panels, and replacing the dataset from this currently seems to be keeping the conditional formatting settings. Why is the functionality from importing data here different than importing data from the other panels? Will be sure to continue using the Data panel for this but want to understand for when questions come up as I help others with this and share best practices.

Thanks for that detail. 

This is similar to a long list of features with data linked shapes and dynamic shapes that i’ve been asking for. I’m afraid we are both at the technical limit of the smart object functionality. They are promising a lot of updates to this coming soon. 

I’m going to try and see if i can reproduce it…  So i can setup the test: 

1. Does your imported data have a unique value column like an ID that could be used to maintain identity attachment to your shapes?
2. Are you open to making your conditional rules more complex to be able to just ‘apply to all shapes’ after a reload?
   1. I do this by selectling the rule and dragging a selection of the whole shapes/screen that i want my rules to apply to if they have gotten disconnected.

Thank you for confirming that this functionality is currently not available. Look forward to seeing what those updates are soon!

1. The imported data has a unique value column.
2. The conditional formatting rules are set up in a way where they are complex enough to apply to all shapes. I am not able to click and drag a selection of the conditional formatting settings, only the Ctrl up / down keys seem to work which does not move it to the apply to all so I am still having to select one at a time to apply the rule to all.