Factorio Forums

In /editor mode, an upgrade planner which specifies upgrade paths for both beacons and modules will upgrade only beacons.
Modules are not targeted by the same upgrade planner until all beacon upgrade paths have been exhausted.
An upgrade planner which specifies only module upgrades functions normally.

In regular play mode, both beacons and modules are correctly marked for upgrade by the same upgrade planner.
Tested on 2.1.7 with minimal mods.

Thanks for the report. This is simply how instant-upgrading works when in the editor. Because upgrading the beacon invalidates the old beacon the upgrade logic no longer has any way to upgrade the modules (since it can't see the instant-upgraded new beacon). I don't currently have any way to make this work nicer.