The lens refractive index in the Huygens Software refers to the Refractive Index (r.i.) of the medium in which the microscope objective is immersed (the Lens Immersion Medium). Objectives are designed to work on particular immesion media, like oil (r.i. ~ 1.51), water (r.i. ~ 1.34) or air (r.i ~ 1.00).
The lens r.i. is directly related to its Numerical Aperture.
A mismatch between the refractive index of the Lens Immersion Medium and Specimen Embedding Medium (with the Medium Refractive Index) will cause several serious problems: see Acquisition Pitfalls.
For dry lenses (or air lenses) see Air Lens Correction.
(This is part of the Microscopic Parameters).