JohnR
I began flying pre-JAR as a PA on both PA23 and PA31 both well over 2000kg as you mentioned. All the flights were AOC light freight (mail etc.) or pax both day and night flight (normally night! when no one else wanted the job!).
We very rarley had to obain an IFR service and as expected were not charged for it day or night!
I would give them a call and get it sorted out, the last incorrect invoice I got came from Edinburgh, they were very polite and got it sorted for me.
Cheers........