Using the 0.17 version still, so maybe it's fixed in a later version. Automatically marks the "belt elevators" to move between underground levels for upgrading and breaks their connection. Tried adding a filter but it had no effect that I could tell. Item name is "subterra-[normal belt name]-up/down/out". For example, I started making express belts, and my fast belt elevators, called "subterra-fast-transport-belt-down" were replaced by them, as well as "subterra-fast-transport-belt-up" and "subterra-fast-transport-belt-out". Works great otherwise, thanks for your work.

The only thing this mod does (at 0.17+) is mark belts for upgrade as if they were marked by an upgrade planner. The actual swap happens via robots with no scripting magic. You can try testing SubTerra belt elevators without my mod using an upgrade planner to see if they still break. If so, the problem lies with SubTerra.

Just wanted to say that, though I've had to stop using SubTerra since Factorio 1.0, the fix to this problem would be ignoring the entities with names of the format "subterra-{speed}-transport-belt-{direction}". I'm not sure if the entity.next_upgrade property works in SubTerra normally since they're made up of linked entities on different surfaces, but it would be great if you could find the time to expand the entity filter settings feature a bit to, for example, ignore entities with names starting with given strings ("subterra-"), or by ignoring those whose names match a configurable string.find comparison. I'm sure there are many entities from other mods that would benefit from this feature as well.