All you can do is to make the necessary from the Script editor (Add Defect Field Cust) and apply changes.
I am suggesting this because, you already informed that the code is been cleared off and still getting the customized part.
OR.
Check the Entire Defect Module code, it must be referring to somewhere.
Note: I had this kind of issue earlier, I have created a new project and performed the same, worked fine. Some times ALM behaves weird in Workflow vertical, the same Piece works fine in one and doesn't trigger in few.
I suggest you to do the same in a fresh project or make the same changes from the Script Editor(Add Defect Field Cust) and give a try.