Hi Kelli, welcome to OB! What you are seeing is a pretty standard response Dendrobiums have to any kind of stress or change in their environment. Unless the bare canes are black and look like they have some bacterial rot I'd leave them. The plant will use those as reserves and draw energy from them while it tries to re-establish it's root system. Repotting was a good thing even though Dens don't generally like that. Did you cut off the rotten roots before repotting? Dens tend to be top heavy. Stick it new pot and all into a heavier clay pot. That should help balance it out.
Your Den is a Phal type and likes to be warm, in bright light (not direct sun), and is a heavy feeder during it's active growth cycle. It doesn't require a winter rest like some of the other Dens. I just reduce the water and fert in the winter months.
If you post a pic we can get a better idea of what you're dealing with, and maybe have some more specific answers for you.