Hey there!
This is a known issue in the engine and it should be addressed in 5.6. The bug had to do with the equals operator when we determined which Input Modifiers/Triggers to recreate versus which to persist when control mappings were rebuilt.
I would still mostly recommend adding your triggers and modifiers in the Input Mapping Context itself though, as often times you may want different ones for gamepad versus keyboard/mouse mappings.
Thanks,
Ben