Welcome to the forum!
Gosh, I didn't answer this the other day, because I'm not sure if I know the answer. It looks like no one else knows either.
When you say that you've solved it before by indexing the colors, what does that mean exactly?
The only thing I could suggest would be to remove the gradients before you use Trace Bitmap, and replace them afterwards. Or else if you can't remove them first, then just do the trace, and delete the unwanted parts after. And then replace the gradients.