Using /bobby upgrade can be very slow, even if you have a good CPU

A potential fix would be to multithread the chunk upgrading process by splitting the world in the same amount of parts that you have threads

The actual upgrade process is already multithreaded. Minecraft's reading/decompression and writing/compression code however is limited to a single thread, and I suspect that's the bottleneck in your case. Not much I can do about that without re-implementing all of that, and that's too out of scope imo given it'd only really help for this one, relatively infrequent, procedure.