Bug upgrade/downgrade doesn't work on belt weaving when in a project.
Simple test, weave red and yellow undergrounds, then run an upgrade planner. Works outside of projects, but in project, messes up and an undo doesn't fix it.

This might not be a bug -- upgrading a belt-weaving underground is disallowed as it could break underground belt weaving. Allowing this makes ensuring that undergrounds are in the correct orientation really hard. As in, depending on the order you place blueprints, the underground belt's direction can be different...
You can perhaps work around this this by deleting and underground and re-placing it.

Let me know if this doesn't work for you, or if you think there is still a bug.

An possible change is to make the underground handling an option instead of always-on, but then ensuring underground consistency becomes the player's responsibility instead.

To clarify, i am not trying to get the blueprint to upgrade/downgrade. I just changed my mind and wanted to use a different tier of belts. The on-screen/live version doesn't upgrade correctly if you are in a project. This happens on stage 1 the first time the undergrounds are placed, even when that is the only thing in the project. The workaround is to use a filtered upgrader and do one belt first, then the other.