According to the research of Narciso Yepes (guitarist and lutenist) who made the first complete recording of Bach's lute works, first on the lute, then on the guitar:
Instrumentation and tuning that Bach may have intended for his lute works, or at least that solves their technical problems:
BWV 995 (G minor)
14-course theorbo-lute
tuning: f'-d'-a-f-d-A-G-F-Eb-D-C-Bb1-A1-G1
BWV 996 (E minor)
13-course lute
tuning: g'-e'-b-g-e-B-A-G-F#-E-D-C-B1
BWV 997 (C minor)
13-course lute
tuning: g'-eb'-c'-g-eb-c-G-F-Eb-D-C-Bb1-Ab1
BWV 998 (E-flat major)
14-course theorbo-lute
tuning: g'-eb'-bb-g-eb-Bb-Ab-G-F-Eb-D-C-Bb1-Ab1
BWV 999 (C minor)
10-course lute
tuning: f'-d'-a-f-d-A-G-F#-Eb-D
BWV 1000 (G minor)
13-course lute
tuning: f'-d'-a-f-d-A-G-F-Eb-D-C-Bb1-A1
BWV 1006a (E major) PRELUDE
14-course theorbo-lute
tuning: g#'-e'-b-a-e-B-A-G#-F#-E-D#-C#-B1-A1
BWV 1006a (E major) SUITE
14-course theorbo-lute
tuning: g#'-e'-b-g#-e-B-A-G#-F#-E-D#-C#-B1-A1