This is a known limitation. Was upgrading possible in earlier versions? Which version(s)? Fast-replacement got disable in 0.0.7 according to the changelog, and I think this means that upgrading was also disabled then.
I hope to fix it in version 0.1.0, but currently 0.1.0 allows connecting different levels of linked belts via up/downgrading which I would like to fix. Let me know if you are willing to allow that if it lets you upgrade belts.