Quick update on this. Thanks to a phone call from Mark Pollitt, I have managed to do this. Very briefly, the process was as follows:

1. Build a rucksack with the LBAP taxa
2. Add a new taxon designation type term list for the LBAP species
3. Run batch update 'Des2' to assign the taxa from the rucksack to the new LBAP designation (you'll need to first get the key of your new designation from the 'taxon_designation_type' table)
4. Rebuild the taxon designation index

Now you should be able to run the batch update 'Des1' to associate the new LBAP designation with a designation group. Unfortunately that doesn't seem to work. Mark has already reported this as a bug. The workaround is:

5. Manually edit the 'taxon_designation_set_item' table, inserting a new row to associate the new designation with the designation set of your choice (first you need to get the keys of these items from the 'taxon_designation_type' and 'taxon_designation_set' tables respectively).
6. Rebuild the taxon designation index

I just associated by new LBAP designation with the existing 'Biodiversity Action Plan species (2007)' designation set. Mark created a new designation set which means a few extra steps above.

I'm not sure if step 4 was necessary at that point or not.

Rich