I joined 99 Sqn in September 1959 and looking at my log book the three C Mk 2 Britannias (392, 398 and 404) were used extensively to convert / train former Hastings pilots and crews onto type. ISTR the C Mk 2s lacked the freight door and strengthened floor of the C Mk 1s so were limited to training or Pax only loads.
My logbook shows one overseas (conversion) training flight to Nicosia in October 1959 in 398 and after that C Mk 1 flights predominated. Thereafter my log book shows the occasional overseas flights in a C Mk 2, but limited to Pax only.
I assume the later overseas training flights you refer to were route provers or with crews being converted to type.