Eww, that Recorder 3.3 checklist will cause problems forever more! I think the stance I usually take is that if any mistake in the checklist is causing grief outside the list (in R6 etc) or a name needs amending to prevent extra synonymisation elsewhere then that is doable. But I don't routinely correct the many mistakes in things like the hierarchy because it's a can of worms ;)
As to the parent child relationships between species and species-sensu-latu, generally speaking an s.l. shares the same parent as the species that form the concept if they all share the same genus - otherwise it points to the next shared parent. Any other arrangement gets very tricky to maintain and causes no end of trouble ... keep it simple :D
Chris Raper, Manager of the UK Species Inventory, Angela Marmont Centre for UK Biodiversity,
Natural History Museum, Cromwell Road, London, SW7 5BD. (tel: 020 7942 5894)
also Tachinid Recording Scheme (http://tachinidae.org.uk/)