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.

I know the mod is primarily developed for personal use, but I thought you might want to know about this interaction.

I will take a look

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).