I am wondering if the "cryogenic helium" system discussed in articles about the 1-Sept-2016 SpaceX Falcon 9 anomaly (see this answer for a good summary to date) is not actually related to the high pressure gaseous helium in the COPVs which were moved inside of the LOX tanks, but instead this is actually for liquid helium used in more standard cryogenic applications, to either maintain the sub-cooled LOX well below its boiling point, or for fast pumping speed cold trapping or cryopumping.
Looking at a typical Falcon 9 countdown timeline from here as linked in this answer, I've pasted a selected, discontinuous subset of items below. You should go to the original link for the complete thing.
This filling near the end seems like a bad idea for an extremely high pressure, heat generating pressurization of the COPVs which will end up swimming in sub-cooled LOX. Instead, this looks like filling and later topping off of cold traps.
Is this Liquid helium for cold trapping and cryopumping? Are there mechanical compressors or is this just dewar-supplied LHe?
T-0:33:30 Stage 1 Liquid Oxygen Loading
T-0:29:30 Stage 1 Helium Load
T-0:25:00 All three Cryo Helium Pumps active
T-0:22:00 Stage 2 Fuel Loading Complete
T-0:19:30 Stage 2 Liquid Oxygen Loading
T-0:17:20 Stage 1 LOX Flowrate Adjustment for Stage 2 Fast Fill
T-0:13:15 Stage 2 Helium Loading
T-0:13:00 Stage 2 LOX Flow Adjustment for Helium Cryo Load
T-0:09:15 Stage 1 Helium Topping
T-0:06:45 Stage 2 Helium Transition to Pipeline
T-0:01:25 Helium Loading Termination