I have the mod 'Junk Trains' (junkRails) https://mods.factorio.com/mods/goldsword44/JunkTrain
I was building a base using these, and ran into a train stop deadlock issue that really has no reason to be an issue given the segmentation of the tracks... so I posted a bug about it; but the wanted me to make a version that would work in vanilla; remembered this upgrade planner, so I saved the map, converted to a scenario, added some chests with regular rails, reloaded that map, and started upgrade planning.
when I use a blueprint with scrap rails converted to regular rails, I get a message 'unknown key: blueprint-upgrade successful' but the blueprint still has scrap rails in it. Using the upgrade planner tool ( I found in craft menu and made one) it doesn't upgrade the rails either.
Also doesn't seem able to select the trains to replace junk locomotives with regular locomotives....

Just though I'd let you know; I'm giving up now so it's no sort of priority.

The same happens with the 'Power Rail's that come with the 'RailPowerSystem' mod (https://mods.factorio.com/mods/Hermios/RailPowerSystem). I think the problem might be that you are using the items instead of the entities. I say this because, in the filtered deconstruction planner, you have to select both the straight and curved rail sections separately, while in the upgrade planner you can only select the straight rail. More might be needed for the Power rail than that, though, I'm not sure...