Hello Nicolette,
Sorry for my delayed response. Back from vacation, but sicker than a ... very sick bird. 
Nick, of course, is correct. Just let the import continue to run until you get the completed message. This can take 1-2 hours where BD appears to be hung. Let it run. You will get a message indicate how many were added and how many were removed. This World bird checklist with all subspecies is a LOT of data and takes a long time to import.
And, just to be sure I understand you text correctly, your database contains everything. All your sightings and all of your tax lists. So, if you import the new Clements into one database, and then copy the database over to another system, then it will be there also - you will just need to activate the tax list if it hasn't been activated on the new system yet.
Also, yes, each system remembers your settings even if you uninstall and re-install BD.
Let me know if I can assist further.
Jeff |