I haven't attempted to upgrade any of my reports... since the old and new Report Builder can run in parallel, I didn't have a lot of need to add that particular workload, but if I need to create a new report I will try the new one first.
That said, can you confirm that you can find all your segments in the Components area of Adobe? Maybe the segment has been accidentally deleted? Or maybe there is a bug that makes the new tool think it's incompatible?
Without seeing your report or what is in your components, we will have limited visibility... but I will do my best to help.