Yes!
Cut the rotted area out as soon as you can. This will spread even more, if left unchecked.
I just finished a similar "operation" on my Vanilla planifolia. I read up on the post (and various links), in the thread I have placed below:
rooting a vanilla vine?
I followed the suggestions and made the cutting in the middle of the rotted area. I sterilized my clippers and cut up to the first healthy node on the clipping. Then placed the fresh cut end in Horticultural Sulphur, I had a pot with a mix media (my own mix up) already watered and ready with a set stake for the new vine.
After planting the new cut vine, I cut to the first healthy node (sterilized the clippers again first) on the "mother" plant.
Now I have 2 Vanilla planifolias (OMG! one's MORE than enough!!!), though I know a member of the Orchid Society I belong to who wants a Vanilla. So I will ask him if he's interested in a trade for one of his propagated orchids (everyone is happy then!).
Just FYI "Kethry1313", I don't know how much you know about the Vanilla species.
They are MONSTERS!
Seriously!!
When I first got mine it was 18" tall. I put it out in the middle to late summer, and at the time I brought it into the house for the autumn cold weather. It was almost 5' tall. These orchids are the fastest (I believe?!?) as well as the largest (can get over 60' tall/long?) growing orchids. The flower, funny enough, from my "research", smells like dirty socks and only last upto 24hrs.
I built a "trellis" for it to grow up, with a little help in tying it to the trellis every few nodes.
I am actually morbidly fascinated in what will happen to it when I put it outside once the last spring frost is done.
If it grew almost 4' in about 2-3 months...what will 5-6 months do to it!!!
Anyway, if you can save both cuttings "Kethry1313" (like I have). Then you have a trader for someone else...or you can have 2 Vanillas in your home.
allaKAZAAM