Did you use a breakpoint and debug to see if you are getting the correct data in your microflow?

There could be several issues.

Your data is retrieved, but because of access rights, the user is not able to see the attribute values

Your data is retrieved, but certain objects are not refreshed to allow displaying the associated data

Somehow the association between checkboxes and sample_data is not stored.

By the way, you are associating sample_data to the Helper object, I don't think you need to associate the checkboxes object as well, because that information can be retrieved via the existing Checkboxes_Sample_Data association.

Two additional best practice tips (free of charge): Only use singular for Entities (that way it is easier to see if you are getting an object or a list of objects in a retrieve) and try to avoid _ in an Entity name, because you might get confused with association names