Ok, I resolved this. Couple of things to try – Ensure that the order of conditionals is correct, I had mine a bit messed, was adding an item in the middle instead of appending it to the end. I also increased the max_input_vars tp 6000 and threw the max_input_nesting_level to 10000.. I cannot say if they made a difference, I have limited time to test, I’m fairly confident that its the order that caused it to remove conditionals…
I have the same issue. I can save 2 lines conditional options but adding a 3rd conditional requirement fails and the new ruels are not saved.