So I’ve had a look at the pipeline you posted and I’m hoping I understand what you want to do in it. I think the issue here is that you are trying to filter the related objects which I think isn’t really possible…? If you are sure that’s exactly what you were doing before and it worked then I have no explanation for that BUT to move forward, if you what you are wanting to do here is get the EEA1 objects that are inside the Transfected_Cell objects then the “Select objects to filter” should be the EEA1 objects and then you set the filter to “Limits” “Parent” and “Transfected_Cells” with a minimum value of 1. Then the resulted objects will be EEA1 objects that found within Transfected_Cells
But actually, I think if you are trying to do with Relate and Filter modules is correct then the better option would definitely be MaskObjects. This module allows you to delete the objects or portions of objects that are outside of other objects, is slightly easier to understand in terms of the resultant objects and also is only one module instead of 2!