Hello Rob,
What is the Vdd level when you attempt to clear the low voltage warning? Is your setting for bits LVDV:LWWV within SPMSC2 register appropriate to your operating voltage? Otherwise, I cannot see any reason why the LVWF flag should not be cleared.
Within the ISR, it may also be a good idea to re-write the LVDV:LVWV bit settings, just in case they might become corrupted over an extended period of time.
Regards,
Mac