It looks like the medium it is in is too soggy, and does not allow any aeration for the roots of the plant.
It is best to cut out the infected area, let the cut area of the plant harden, and then try to get the base of the plant to re-root in a medium that aerates better than what it is in now... This rooted portion of the plant will grow like a terrestrial, as long as the medium is well aerated.
The remainder of the plant will grow as an epiphyte. The top of the plant likes full sun, to stimulate flowering.
Vanilla is pretty hardy, and re-grows well from cuttings, so you have a very good opportunity to save this plant!!!
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