One Import Script for UDSElement

Summary:

I'm trying to load LUDs using the UDSElement template, but for my current setup all the records have to be in 1 file. Example of the selection list I'm trying to load are Employee ID, Job ID, and Position ID, but when I was running for position ID and then the others were getting inactivated. After I combined all three selection lists into 1 file, ran the script then it does inactivate the missing values. Is this how the UDSElement entity works when loading or do I have an incorrect setting?