When using the rail planner (https://mods.factorio.com/mod/RailSignalPlanner) on a rail near a rift portal, the rail planner can delete the portal. It leaves behind the two internal signals of the rift rail, which then cannot be removed or built over.

The dev of rift rail gave this explanation https://mods.factorio.com/mod/RiftRail/discussion/6aa03d5ddc7d0a6170e2298a:
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I investigated the interaction and here is what actually happens:

Why the portal disappears: RailSignalPlanner forcefully deletes the portal's internal signals during its graph planning. RiftRail has an intentional safeguard where any missing internal component triggers a clean self-destruction of the whole portal, rather than leaving a broken, unusable structure behind.
Why the signals remain: RailSignalPlanner creates those two signals back at the end of its routine. But since the portal was already gone and these internal signals are non-interactable by design, they become stuck orphans.
The portal self-destruction on component loss is a core design choice I intend to keep. The proper way to handle this would be for the rail planner mod to simply ignore internal/indestructible signals altogether.

For the leftover signals currently stuck in your world, unfortunately the only way to remove them is via the Map Editor (/editor).
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Would this be possible to implement?