Yes they don't like to be waterlogged. Sometimes when the rot gets in, there's just nothing you can do, the diseased plant seems to attract more trouble as it goes down.
So long as it's now in a free-draining material, which was pretty sterile, and if the roots - when you repotted it - didn't show evidence of other damage - insect invasion etc, then it might settle and stabilise.
If you have anything that you can use such as an anti-fungal dusting powder, or failing that, cinnamon from your kitchen pantry, I would take the big breath and slice off the decaying part about 1/4 inch below, dust well and leave and fingers crossed that it will heel over and make new off-shoots. (You may be able to save some cuttings to root or graft but they don;t get the same caudiform shape as when grown from seed)
Sad but you can't always save a plant, adenium are very hard once they get rot problems, this worked for me in about 1/2 cases when I got a lot of small plants innundated at a wrong season. At least you are going into growth now?
Good luck hope you get more responses before acting.

An ocean of information at the link below.

Here is a link that might be useful: nr.sundaram. Benadeniums.