In theory Sampletank should only use one of those sets of files. I don't have Sampletank here, so I can't be more specific, but there likely is a setting in Sampletank to specify where it gets the files from.

If not, the easy way would be to delete one folder (don't empty the trash), run BIAB, open a song with a MIDI Supertrack in it (or manually add a Hi-Q instrument) and see if it works - if it doesn't then restore the folder you deleted and delete the other.

I work here